Method and composition for diagnosis or treatment of aggressive prostate cancer

ABSTRACT

Methods, pharmaceutical formulations and medicaments for treating prostate cancer or preventing the progression of a nonaggressive form of prostate cancer to an aggressive form, in a mammal, include a therapeutically effective amount of one or more active agents that reduce the expression or biological activity of both Forkhead box protein M1 (FOXM1) and Centromere protein F (CENPF) or biologically active fragments thereof or biologically active fragments thereof selected from the group consisting of an isolated shRNA, siRNA, antisense RNA, antisense DNA, Chimeric Antisense DNA/RNA, microRNA, and ribozymes that are sufficiently complementary to either a gene or an mRNA encoding either FOXM1 or CENPF proteins. A method is also presented for discovering synergistic master regulators of other phenotype transitions, wherein the master regulators are conserved among different species.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit of Provisional Appln. 61/966,271, filed Feb. 19, 2014, the entire contents of which are hereby incorporated by reference as if fully set forth herein, under 35 U.S.C. §119(e).

STATEMENT OF GOVERNMENTAL INTEREST

This invention was made with Government support under CA084294, U54 CA121852 and CA154293 awarded by the National Institutes of Health. The Government has certain rights in the invention.

BACKGROUND

Cancer is not a single entity but rather a highly individualized spectrum of diseases characterized by a number of genetic and genomic alterations (Hanahan and Weinberg, 2011). Distinguishing molecular alterations that constitute true drivers of cancer phenotypes from the multitude that are simply de-regulated has proven to be a daunting task, which is further exacerbated by the complexity of elucidating how such drivers interact synergistically to elicit cancer phenotypes. Prostate cancer is particularly challenging because its notorious heterogeneity, combined with a relative paucity of recurrent gene mutations, has made prostate cancer especially difficult to identify molecularly distinct subtypes with known clinical outcomes (Baca et al., 2013; Schoenborn et al., 2013; Shen and Abate-Shen, 2010). Additionally, while early-stage prostate tumors are readily treatable (Cooperberg et al., 2007), advanced prostate cancer frequently progresses to castration-resistant disease, which is often metastatic and nearly always fatal (Ryan and Tindall, 2011; Scher and Sawyers, 2005).

It should be noted that several factors, including an increase in the aging population and widespread screening for prostate specific antigen (PSA), have contributed to a substantial rise in diagnoses of prostate cancer. The primary means of determining the appropriate treatment course for men diagnosed with prostate cancer still relies on Gleason grading, a histopathological evaluation that lacks a precise molecular correlate. While patients with high Gleason score (Gleason ≧8) tumors are recommended to undergo immediate treatment, the appropriate treatment for those with low (Gleason 6) or intermediate (Gleason 7) Gleason score tumors remains more ambiguous. Indeed, although the majority of Gleason grade 6 tumors, as well as many Gleason grade 7 tumors, are likely to remain indolent (i.e., low-risk, non-aggressive or non-invasive), a minority (˜10%) will progress to aggressive disease.

Indeed, the current lack of reliable and reproducible assays to identify tumors destined to remain indolent versus those that are aggressive, has resulted in substantial overtreatment of patients that would not die of the disease if left untreated. Consequently, “active surveillance” has emerged as an alternative for monitoring men with indolent prostate cancer, with the goal of avoiding treatment unless there is evidence of disease progression. The obvious advantage of active surveillance is that it avoids overtreatment; however, the potential concern is that it may miss the opportunity for early intervention for patients with aggressive tumors. Therefore, better methods with a molecular correlate for diagnosing aggressive prostate cancer have great value.

SUMMARY

Applicants have determined that there is a need to identify molecular determinants of cancers, including but not limited to, aggressive prostate cancer subtypes, a need to identify other prognostic biomarkers of disease outcome, and a need to treat such cancers. The subject matter disclosed herein addresses this need.

In a first set of embodiments, a method for treating prostate cancer or preventing the progression of a nonaggressive form of prostate cancer to an aggressive form, in a mammal, includes administering to the mammal a therapeutically effective amount of one or more active agents that reduce the expression or biological activity of both Forkhead box protein M1 (FOXM1) and Centromere protein F (CENPF) or biologically active fragments thereof or biologically active fragments thereof selected from the group consisting of an isolated shRNA, siRNA, antisense RNA, antisense DNA, Chimeric Antisense DNA/RNA, microRNA, and ribozymes that are sufficiently complementary to either a gene or an mRNA encoding either FOXM1 or CENPF proteins.

In a second set of embodiments, a pharmaceutical formulation for treating prostate cancer or reducing or preventing the progression of a nonaggressive form of prostate cancer to an aggressive form, includes a therapeutically effective amount of one or more active agents that reduce the expression or biological activity of both Forkhead box protein M1 (FOXM1) and Centromere protein F (CENPF) selected from the group consisting of an isolated shRNA, siRNA, antisense RNA, antisense DNA, Chimeric Antisense DNA/RNA, microRNA, and ribozymes that are sufficiently complementary to either a gene or an mRNA encoding the FOXM1 or CENPF protein.

In a third set of embodiments, a medicament treating prostate cancer or reducing or preventing the progression of a nonaggressive form of prostate cancer to an aggressive form, includes one or more active agents in a therapeutically effective amount that reduce the expression or biological activity of both Forkhead box protein M1 (FOXM1) and Centromere protein F (CENPF) or biologically active fragments thereof selected from the group consisting of an isolated shRNA, siRNA, antisense RNA, antisense DNA, Chimeric Antisense DNA/RNA, microRNA, and ribozymes that are sufficiently complementary to either a gene or an mRNA encoding either FOXM1 or CENPF proteins.

In another set of embodiments, a method includes receiving, automatically on a processor, data that indicates human gene expression profiles for human tissue in a context of interest comprising a plurality of cell phenotypes including at least one gene expression profile representing a first cell phenotype and at least one other gene expression profile representing a second cell phenotype. The method also includes determining, automatically on a processor based on the human gene expression profiles, data that indicates an interactome of human tissue in the context of interest and data that indicates a human signature that represents a ranking of genes differentially expressed in the second cell phenotype compared to the first cell phenotype. The method also includes determining, automatically on a processor based on the interactome of human tissue and the human signature, data that indicates human master regulator molecules most likely to have produced the human signature. The method further includes receiving, automatically on a processor, data that indicates animal model gene expression profiles for animal tissue in the context of interest based on multiple in vivo perturbations of one or more genetically distinct animals including at least one gene expression profile representing the first cell phenotype and at least one other gene expression profile representing the second cell phenotype. The method still further includes determining, automatically on a processor based on the animal model gene expression profile, data that indicates an interactome of animal tissue in the context of interest and data that indicates an animal signature that represents a ranking of genes differentially expressed in the second cell phenotype compared to the first cell phenotype. Even further, the method includes determining, automatically on a processor based on the interactome of animal tissue and the animal signature, data that indicates animal master regulator molecules most likely to have produced the animal signature. The method next includes determining, automatically on a processor based on the human master regulator molecule and the animal master regulator molecules, data that indicates conserved master regulator molecules that are most likely to have produced both the human signature and the animal signature. In some embodiments of this set, the method yet further includes determining, automatically on a processor based on the conserved master regulator molecules, data that indicates two or more synergistic conserved master regulator molecules that have a net combined effect greater than a sum of individual effects.

Still other aspects, features, and advantages of the invention are readily apparent from the following detailed description, simply by illustrating a number of particular embodiments and implementations, including the best mode contemplated for carrying out the invention. The invention is also capable of other and different embodiments, and its several details can be modified in various obvious respects, all without departing from the spirit and scope of the invention. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.

BRIEF DESCRIPTION OF THE DRAWINGS

The present invention is illustrated by way of example, and not by way of limitation, in the figures of the accompanying drawings and in which like reference numerals refer to similar elements and in which:

FIG. 1A is a block diagram and graph that illustrate example gene profiling data for multiple human subjects with various stages of prostate cancer, according to an embodiment;

FIG. 1B is a block diagram and graph that illustrate example gene profiling data for multiple mouse models for prostate cancer, according to an embodiment;

FIG. 1C is a block diagram and graph that illustrate example effects on gene profiling data for mouse models in response to various perturbagens, according to an embodiment;

FIG. 2A is a block diagram and graph that illustrate example interactomes for human and mouse models with prostate cancer, according to an embodiment;

FIG. 2B is a graph that illustrates example percentage of the interactomes that are conserved between human and mouse models with prostate cancer, according to an embodiment;

FIG. 3A is a Venn diagram and table that illustrate example selection of a subset of master regulators from a full set determined by available automated computer processes, according to an embodiment;

FIG. 3B is a diagram that illustrates example ranking of master regulators for their impacts on prostate cancer, according to an embodiment;

FIG. 3C is a table that illustrates example ranking of master regulators for their impacts on prostate cancer by various available algorithms, according to an embodiment;

FIG. 3D is a table that illustrates example predicted synergy of FOXM1 and CENPF among the subset of master regulators using available algorithms, according to an embodiment;

FIG. 4A and FIG. 4B are flow charts that illustrate an example method for determining various synergistic master regulators for other phenotype transitions, according to an embodiment;

FIG. 5 is a table that illustrates example clinical datasets used to determine whether synergistic master regulators FOXM1 and CENPF are prognostic biomarkers of prostate cancer outcomes, according to an embodiment;

FIG. 6A is an image that illustrates example micrographs of FOXM1 and CENPF stained tissues showing enhanced concentrations of both in aggressive prostate cancer tumors compared to other prostate tumors, according to an embodiment;

FIG. 6B is an image that illustrates example micrographs of FOXM1 and CENPF stained tissues showing enhanced concentrations of both in metastasized lung and liver tumors, according to an embodiment;

FIG. 6C through FIG. 6E are graphs that illustrate example Kaplan-Meier survival analysis based on protein expression levels of FOXM1 and CENPF with respect to time to biochemical recurrence, time to prostate cancer-specific death, or time to metastatic progression, respectively, according to an embodiment;

FIG. 6F and FIG. 6G are graphs that illustrate example Kaplan-Meier survival analysis based on the interactome-inferred activity levels of FOXM1 and CENPF with respect to time to biochemical recurrence, or time to prostate cancer-specific death, respectively, according to an embodiment;

FIG. 7 is a table that illustrates example prognostic power of coexpression of protein levels of FOXM1 and CENPF, with death due to prostate cancer and time to metastasis as evaluation endpoints, according to an embodiment;

FIG. 8 is a flow chart that illustrates an example diagnostic method for determining whether a subjects is at risk based on coexpression of the synergistic master regulators FOXM1 and CENPF, according to an embodiment;

FIG. 9A is a graph that illustrates example resulting relative mRNA expression levels for the shared targets of FOXM1 and CENPF in the indicated cell lines following individual or co-silencing of FOXM1 and CENPF, according to an embodiment;

FIG. 9B is a graph that illustrates example enrichment of FOXM1 binding normalized to input with and without silencing of CENPF, according to an embodiment;

FIG. 9C is an image of micrographs that illustrate example changes in subcellular localization of FOXM1 and CENPF proteins in prostate cancer cells after silencing either, according to an embodiment;

FIG. 10 is a flow chart that illustrates an example method for determining coexpression of the synergistic master regulators FOXM1 and CENPF, according to an embodiment;

FIG. 11A is a block diagram that illustrates an example in vitro treatment using lentiviral silencing vectors expressing shRNA for FOXM1 or CENPF or both or a control, according to an embodiment;

FIG. 11B is an image of Western blots that illustrate effectiveness of lentiviral silencing vectors, according to an embodiment;

FIG. 11C is an image of photographs that illustrate DU145 cell colonies, visualized using crystal violet, are drastically reduced by silencing both FOXM1 and CENPF compared to other combinations, according to an embodiment;

FIG. 11D is graph that illustrates the quantitative number of DU145 cell colonies are drastically reduced by silencing both FOXM1 and CENPF compared to other combinations, according to an embodiment;

FIG. 11E is a block diagram that illustrates an example in vivo experiment based on tumor growth in the presence of silencing either FOXM1 or CENPF or both, according to an embodiment;

FIG. 11F is a graph that illustrates example in vivo tumor volume growth in the presence of silencing both is more than additive of the effects of silencing either FOXM1 or CENPF separately, according to an embodiment;

FIG. 11G is a graph that illustrates example in vivo tumor weight at time of sacrifice in the presence of silencing either or both FOXM1 or CENPF, according to an embodiment;

FIG. 11H is an image that illustrates example micrographs of tumors form several mice on identical distance scales in the presence of silencing either or both FOXM1 or CENPF, according to an embodiment;

FIG. 11I is a block diagram that illustrates an example in vivo competition assay in which equal numbers of DU145 cells expressing the control shRNA (control cells), or the experimental shRNA for FOXM1 or CENPF or both (experimental cells) as well as red or green reporters (RFP or GFP, respectively) were implanted into mouse hosts, according to an embodiment;

FIG. 11J and FIG. 11K are graphs that illustrate example fluorescence-activated cell sorting (FACS) plots showing the percentage of red cells (R, FOXM1 silenced), green cells (G, CENPF silenced) or yellow cells (Y, both silenced) relative to the total number of fluorescent cells for control tumors and experimental tumors, respectively, according to an embodiment;

FIG. 11L and FIG. 11M are graphs that illustrate example percentages of red, green or yellow cells relative to the total number of fluorescent cells for control tumors and experimental tumors, respectively, indicating profound selection against cells silenced for both FOXM1 and CENPF according to an embodiment;

FIG. 11N is an image of Western blots that illustrate example changes in expression of the indicated representative markers of the PI3-kinase and MAP kinase signaling pathways associated with tumor growth in DU145 and PC3 prostate cancer cells after silencing either FOXM1 or CENPF or both, according to an embodiment; and

FIG. 12 is a block diagram that illustrates a computer system upon which an embodiment of the invention may be implemented.

DEFINITIONS

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The practice of the present invention will employ, unless indicated specifically to the contrary, conventional methods of molecular biology and recombinant DNA techniques within the skill of the art, many of which are described below for the purpose of illustration. Such techniques are fully explained in the literature. See, e.g., Singleton et al., Dictionary of Microbiology and Molecular Biology 3rd.sup.ed., J. Wiley & Sons (2001); March, Advanced Organic Chemistry Reactions, Mechanisms and Structure 5th.sup.ed., J. Wiley & Sons (2001); Sambrook & Russell, eds., Molecular Cloning: A Laboratory Manual 3rd ed., Cold Spring Harbor Laboratory Press (2001); Glover, ed., DNA Cloning: A Practical Approach, vol. I & II (2002); Gait, ed., Oligonucleotide Synthesis: A practical approach, Oxford University Press (1984); Herdewijn, ed., Oligonucleotide Synthesis: Methods and Applications, Humana Press (2005); Hames & Higgins, eds., Nucleic Acid Hybridisation: A Practical Approach, IRL Press (1985); Buzdin & Lukyanov, eds., Nucleic Acid Hybridization: Modern Applications, Springer (2007); Hames & Higgins, eds., Transcription and Translation: A Practical Approach, IRL Press (1984); Freshney, ed., Animal Cell Culture, Oxford UP (1986); Freshney, Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications, 6th ed., John Wiley & Sons (2010); Perbal, A Practical Guide to Molecular Cloning, 3rd ed., Wiley-Liss (2014); Farrell, RNA Methodologies: A Laboratory Guide for Isolation and Characterization, 3rd ed., Elsevier/Focal Press (2005); Lilley & Dahlberg, eds., Methods in Enzymology: DNA Structures, Part A: Synthesis and Physical Analysis of DNA, Academic Press (1992); Harlow & Lane, Using Antibodies: A Laboratory Manual: Portable Protocol no. 1, Cold Spring Harbor Laboratory Press (1999); Harlow & Lane, eds., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press (1988); Seethala & Fernandes, eds., Handbook of Drug Screening, Marcel Dekker (2001); and Roskams & Rodgers, eds., Lab Ref: A Handbook of Recipes, Reagents, and Other Reference Tools for Use at the Bench, Cold Spring Harbor Laboratory (2002) provide one skilled in the art with a general guide to many of the terms used in the present application.

One skilled in the art will recognize many methods and materials similar or equivalent to those described herein, which could be used in the practice of the present invention. Other features and advantages of the invention will become apparent from the following detailed description, taken in conjunction with the accompanying drawings, which illustrate, by way of example, various features of embodiments of the invention. Indeed, the present invention is in no way limited to the methods and materials described. For convenience, certain terms employed herein in the specification, examples and appended claims are collected here.

Unless stated otherwise, or implicit from context, the following terms and phrases include the meanings provided below. Unless explicitly stated otherwise, or apparent from context, the terms and phrases below do not exclude the meaning that the term or phrase has acquired in the art to which it pertains. The definitions are provided to aid in describing particular embodiments, and are not intended to limit the claimed invention, because the scope of the invention is limited only by the claims. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

The term “nucleic acid” as used herein refers to any natural and synthetic linear and sequential arrays of nucleotides and nucleosides, cDNA, genomic DNA, mRNA, oligonucleotides and derivatives thereof. The term “nucleic acid” further includes modified or derivatized nucleotides.

An “isolated” nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid molecule, namely cancerous or noncancerous biological samples. An “isolated” nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.

As used herein, “oligonucleotide” refers to an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or mimetics thereof. This term includes oligonucleotides composed of naturally-occurring nucleobases, sugars and covalent internucleoside (backbone) linkages as well as oligonucleotides having non-naturally-occurring portions which function similarly. Such modified or substituted oligonucleotides are often preferred over native forms because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for nucleic acid target and increased stability in the presence of nucleases.

As used herein, an “inhibitory oligonucleotide” includes antisense, siRNA, shRNA, ribozymes and MIRs or other oligonucleotide that reduces the expression of a targeted FOXM1 or CENPF gene or protein.

“Biological sample” refers to a sample of prostate cells. The sample can be prostate cancer cells, for example, those taken from a prostate biopsy from a subject having prostate cancer, or of normal prostate cells either taken from a normal control subject or in some embodiments from a noncancerous area of the prostate of the subject having prostate cancer.

In other embodiments, the biological sample comprises circulating prostate cancer cells isolated from the blood, cerebrospinal fluid (CSF) or serum of a subject having prostate cancer or exosomes derived from prostate cancer cells.

“Indolent prostate cancer” means low-risk, non-aggressive or non-invasive prostate cancers which would not lead to subject death if left untreated.

“Aggressive prostate cancer” means prostate cancer that leads to a shortened life expectancy of the subject or an increased occurrence of metastasis to other tissue cancers.

“At high risk of progressing to aggressive prostate cancer” means that the subject has prostate cancer that, more likely than not, is or will become aggressive prostate cancer.

“Administering” or “administration of” a drug or therapeutic pharmaceutical composition to a subject as used herein means any method known in the art including both direct administration, including self-administration (including oral administration or intravenous, subcutaneous, intramuscular or intraperitoneal injections, local administration directly into or onto a target tissue (prostate tumor or prostate gland) or administration by any route or method that delivers a therapeutically effective amount of the drug or composition to the prostate cancer cells or tumor or tissue to which it is targeted.

Administration of an agent “in combination with” includes parallel administration of two agents to the patient over a period of time, co-administration (in which the agents are administered at approximately the same time, e.g., within about a few minutes to a few hours of one another), and co-formulation (in which the agents are combined or compounded into a single dosage form suitable for oral, subcutaneous or parenteral administration).

A “subject” is a mammal, typically a human, but optionally a mammalian animal of veterinary importance, including but not limited to horses, cattle, sheep, dogs, and cats. In some embodiments a “subject” refers to either one who has been previously diagnosed with or identified as suffering from prostate cancer or to one who does not have prostate cancer, i.e., a normal or control subject.

As used herein, the term “diagnosis” includes the detection, typing, monitoring, dosing, and comparison at various stages of prostate cancer in a subject. Diagnosis includes the assessment of a predisposition or risk of developing an aggressive form of prostate cancer.

A “therapeutically effective amount” of an active agent or pharmaceutical composition is an amount that achieves the intended therapeutic effect, e.g., alleviation, amelioration, palliation or elimination of one or more manifestations of prostate cancer, including aggressive prostate cancer in the subject. The full therapeutic effect does not necessarily occur by administration of one dose and may occur only after administration of a series of doses. Thus, a therapeutically effective amount may be administered in one or more administrations.

As used herein, “active agent” includes any small molecules, polypeptides, antibodies, nucleic acids (including antisense RNA, siRNA, microRNAs, and ribozymes that reduce the expression (including by reducing transcription or translation of the gene or mRNA, respectively) and/or biological activity of FOXM1 or CEPF.

As used herein, the terms “treat,” “treatment,” “treating,” or “amelioration” when used in reference to prostate cancer refer to therapeutic treatments for the prostate cancer, wherein the object is to reverse, alleviate, ameliorate, inhibit, slow down or stop the progression of the prostate cancer to an aggressive form, or reduce the severity of a symptom or condition. The term “treating” includes reducing or alleviating at least one adverse effect or symptom of a condition. Treatment is generally “effective” if one or more symptoms or clinical markers such as prostate-specific antigen (PSA) are reduced.

A “prophylactically effective amount” of a drug is an amount of a drug that, when administered to a subject, will have the intended prophylactic effect, e.g., preventing or delaying the conversion/transition of a non-aggressive prostate cancer to an aggressive prostate cancer. The full prophylactic effect does not necessarily occur by administration of one dose and may occur only after administration of a series of doses. Thus, a prophylactically effective amount may be administered in one or more administrations.

“FOXM1” as used herein refers to Forkhead box protein M1 is a protein that in humans is encoded by the FOXM1 gene. The protein encoded by this gene is a member of the FOX family of transcription factors. FOXM1 is also referred to as FKHL16; FOXM1B; HFH-11; HFH11; HNF-3; INS-1; MPHOSPH2; MPP-2; MPP2; PIG29; TGT3; TRIDENT. The human and mouse reference mRNA sequences are NM_001243088 (SEQ ID NO: 49) and NM_008021 (SEQ ID NO: 51), respectively. The human and mouse protein sequences are NP_001230017 (SEQ ID NO: 50) and NP_032047 (SEQ ID NO: 52), respectively. For the purpose of the methods and compositions of the invention, “FOXM1 protein” includes orthologs (analogs in different species).

“CENPF” as used herein refers to centromere protein F, a protein that in humans is encoded by the CENPF gene. The CENPF protein associates with the centromere-kinetochore complex. The protein is a component of the nuclear matrix during the G2 phase of interphase. CENPF is also referred to as CENF; PRO 1779; hcp-1. The human and mouse reference mRNA sequences are NM_016343 (SEQ ID NO: 53) and NM_001081363 (SEQ ID NO: 55) respectively; and the human and mouse protein sequences are NP_057427 (SEQ ID NO: 54) and NP_001074832 (SEQ ID NO: 56), respectively. For the purpose of the methods and compositions of the invention, “CENPF protein” includes orthologs (analogs in different species).

“Protein expression” refers to expression of protein as measured quantitatively by methods including without limitation Western blot, 2-dimensional SDS-PAGE and mass spectrometry.

“mRNA expression” refers to the expression of mRNA that can be measured quantitatively by methods including but not limited to nuclease protection assays, northern blots, real time quantitative PCR, and in-situ hybridization.

“Control level” and “normal level of expression” as used herein refer to a level or range of levels of FOXM1 or CENPF expressed in normal prostate tissue or indolent prostate cancer tumors.

“Threshold” or “threshold level” as used herein refers to a level or range of levels that separate normal level of expression of FOXM1 and CENPF from a pattern, level or ranges of levels of expression of FOXM1 and CENPF that indicate a high risk of aggressive prostate cancer. When the levels of expression of FOXM1 and CENPF are equal to or greater than the threshold level then it is determined that the subject is at high risk of developing aggressive prostate cancer or has aggressive prostate cancer, and vice versa.

“Protein” as used herein is a generic term referring to and used interchangeably with biologically active native protein, fragments, peptides, or analogs thereof.

“Therapeutic agent” and “active agent” as used herein refer to any inhibitory oligonucleotide, small molecule or compound that reduces the expression or biological activity of FOXM1 or CENPF protein.

“Subcellular localization of FOXM1 and CENPF” as used herein refers to the presence of FOXM1 and CENPF inside a cell. “Colocalization” means that both FOXM1 and CENPF are present in the same cell or if so designated, in the same subcellular compartment, for example colocalization in the nucleus or cytoplasm.

“Master regulator” as used herein refers to a protein that acts to drive any intermediary proteins in a key signaling pathway for a phenotype transition, such as a transition from indolent prostate cancer cell to an aggressive prostate cancer cell.

“Synergistic Master Regulator” as used herein refers to multiple master regulators that together have a measured effect greater than a predicted sum of their individual measured effects.

“Cross-species computational analysis” as used herein refers to automatically searching molecular interaction networks (“interactomes”) of two or more species, such as human and mouse models for human cells, using a computer system to discover interactions present (“conserved”) in both species.

The term “probe” refers to any molecule which is capable of selectively binding to a specifically intended target molecule, for example, an oligonucleotide probe that specifically hybridizes to a prognostic biomarker mRNA such as CENPF or FOXM1, or an antibody that specifically binds CENPF or FOXM1. Probes can be either synthesized by one skilled in the art, or derived from appropriate biological preparations. For purposes of detection of the target molecule, probes may be specifically designed to be labeled, as described herein. Examples of molecules that can be utilized as probes include, but are not limited to RNA, DNA, RNA/DNA chimeras, proteins, antibodies, and organic molecules.

Unless otherwise specified, the terms “antibody” and “antibodies” broadly encompass naturally-occurring forms of antibodies (e.g., IgG, IgA, IgM, IgE) and recombinant antibodies such as single-chain antibodies, chimeric and humanized antibodies and multi-specific antibodies, as well as fragments and derivatives of all of the foregoing, which fragments and derivatives have at least an antigenic binding site. Antibody derivatives may comprise a protein or chemical moiety conjugated to an antibody moiety.

DETAILED DESCRIPTION

A method, composition of matter, article of manufacture and apparatus are described for discovery of synergistic master regulators and the diagnosis and treatment of aggressive prostate cancer. In the following description, for the purposes of explanation, numerous specific details are set forth in order to provide a thorough understanding of the present invention. It will be apparent, however, to one skilled in the art that the present invention may be practiced without these specific details. In other instances, well-known structures and devices are shown in block diagram form in order to avoid unnecessarily obscuring the present invention.

It has been discovered that the genes encoding FOXM1 and CENPF are prognostic biomarkers that are synergistic master regulators of aggressive prostate cancer in humans. Significantly elevated coexpression of both FOXM1 and CENPF genes in a prostate cancer sample at levels at least 35% above control levels is diagnostic of aggressive prostate cancer or of a high risk of developing aggressive prostate cancer, as is described in sample embodiments. Gene expression can be determined by mRNA or protein expression or combinations thereof. Regulatory drivers of prostate cancer malignancy were identified by assembling genome-wide regulatory networks (interactomes) for both human and mouse prostate cancer from expression profiling datasets of human tumors and genetically engineered mouse models, respectively. Cross-species computational analysis of these interactomes identified FOXM1 and CENPF as synergistic master regulators of prostate cancer malignancy that promote tumor growth by coordinated regulation of target gene expression and activation of key signaling pathways associated with prostate cancer malignancy. Thus, coexpression of FOXM1 and CENPF was identified for the first time as a robust prognostic indicator of aggressive prostate cancer with poor survival and metastasis.

Based on the data described herein, certain embodiments of the invention are directed to methods for diagnosing aggressive prostate cancer or a high risk of prostate cancer progressing to an aggressive form if the level of mRNA or protein expression for each of FOXM1 and CENPF in a prostate cancer sample from a subject is at least 35% higher than the corresponding level in a control prostate sample. In another embodiment aggressive prostate cancer is diagnosed if at least 50% of the cells in the prostate cancer sample from a subject express elevated levels of both FOXM1 protein and CENPF protein.

Other embodiments are directed to the treatment of aggressive prostate cancer in a subject by administering therapeutically effective amounts of either inhibitory oligonucleotides or other agent that reduces FOXM1 and CENPF expression in prostate cancer cells or both.

1. Overview

While both FOXM1 and CENPF have been implicated in various cancers, the current work has uncovered a novel synergistic interaction that had not been previously anticipated. FOXM1 encodes a Forkhead domain transcription factor that is frequently over-expressed in many different types of cancer, including prostate, see Alvarez-Fernandez and Medema, 2013; Halasi and Gartel, 2013a; Kalin et al., 2011; and Koo et al., 2012, for reviews. Many previous studies have established a role for FOXM1 expression and activity in the regulation of cellular proliferation, DNA damage, genomic stability, drug resistance, and metastasis, and have shown that FOXM1 interacts with other key regulators such as 3-Catenin and MYB (Lefebvre et al., 2010; Zhang et al., 2011). In particular, the relevance of FOXM1 for prostate cancer has been shown by its gain- or loss-of-function in vivo, which elicit modest effects on tumor growth (Cai et al., 2013; Kalin et al., 2006).

CENPF (also known as mitosin or LEK1 in mouse), a known target of FOXM1, has also been implicated in various cancers, although not previously in prostate, and in some cases has been shown to undergo gene amplification and be associated with disease outcome (see Ma et al., 2006; Varis et al., 2006 for reviews). However, the actual functional role of CENPF has been more elusive and difficult to reconcile. In particular, while CENPF is named for its association with the centromere-kinetochore protein complex, such association is only transient. In fact, CENPF has been shown to have other functions, including regulation of mitosis and cellular proliferation (Bomont et al., 2005; Feng et al., 2006; Holt et al., 2005), which are mediated in part by protein interactions, including with members of the Retinoblastoma gene family as well as with the ATF transcription factor (see Ma et al., 2006; Varis et al., 2006 for reviews).

2. Cross Species Discovery of Regulatory Genes for Aggressive Prostate Cancer

To assemble a human prostate cancer interactome, gene expression profile data reported in (Taylor et al., 2010) was analyzed, which is ideally suited because: (i) it is relatively large (n=185) and diverse, including gene expression profiles from primary prostate tumors, adjacent normal prostate tissue, metastases, and cell lines; (ii) its primary tumors encompass the full range of pathological Gleason scores and have well-annotated clinical outcome data; and (iii) it displays extensive genetic diversity and tumor heterogeneity, as shown by t-Distributed Stochastic Neighbor Embedding (t-SNE) analysis. Several characteristics of this dataset are described below with reference to FIG. 5. Notably, interactomes assembled from three alternative human prostate cancer datasets, also characterized in FIG. 5, were neither as complete nor as extensive. FIG. 1A is a block diagram and graph that illustrate example gene profiling data for multiple human subjects with various stages of prostate cancer, according to an embodiment. Details are set forth in Example 2.

Analysis of genetically engineered mouse models (GEMMs) can circumvent challenges associated with the inherent complexity of the more heterogeneous human cancer phenotypes. Investigations of mouse models of prostate cancer have contributed to characterization of disease-specific pathways, led to the identification of biomarkers of disease progression, and provided useful preclinical models for prevention and therapy (Irshad and Abate-Shen, 2013; Ittmann et al., 2013). Following the description of the first transgenic model of prostate cancer nearly 20 years ago, there are now numerous GEMMs that collectively model key molecular pathways de-regulated in human prostate cancer, and recapitulate the various stages of disease progression including pre-invasive lesions (prostate intraepithelial neoplasia, PIN), adenocarcinoma, castration-resistance, and metastasis (Irshad and Abate-Shen, 2013; Ittmann et al., 2013).

Inherent species differences often hinder direct comparative analyses of mouse models and human cancer. As described herein, a novel combination of computational approaches were applied to enable accurate cross-species integration of regulatory information from mouse to man in the context of prostate cancer. Recent advances in systems biology have led to the reverse engineering of regulatory networks (interactomes) that integrate large-scale datasets encompassing gene expression profiles, protein-protein interactions, genomic alterations, and epigenetic changes associated with cancer and other diseases (see Lefebvre et al., 2012 for a review). While individual analyses of human and murine interactomes led to relevant biological discoveries, cross-species interactome-based interrogation strategies have not been systematically implemented until now.

The results described here are based on an approach for accurate cross-species analysis of conserved cancer pathways based on reverse engineering and interrogation of genome-wide regulatory networks (i.e., interactomes) representing both human and mouse prostate cancer. To accomplish this, the first regulatory network obtained from in vivo perturbation of a repertoire of mouse cancer models was introduced, as well as its comparative analysis with a complementary regulatory network generated from human prostate cancer samples. Cross-species computational interrogation of these paired interactomes followed by experimental validation thus elucidated the synergistic interaction of FOXM1 and CENPF as a driver of aggressive prostate cancer malignancy.

To assemble a corresponding mouse prostate cancer interactome, it was first necessary to generate an appropriately sized gene expression profile dataset representing sufficient expression variability. To address this challenge, 13 distinct GEMMs were first selected, which together represent the full spectrum of prostate cancer phenotypes, including normal epithelium (wild-type), low-grade PIN (Nkx3.1 and APT), high-grade PIN and adenocarcinoma (APT-P, APC, Hi-Myc, NP, Erg-R, and NP53), castration-resistant prostate cancer (NP-AI), and metastatic prostate cancer (NPB, NPK, and TRAMP). FIG. 1B is a block diagram and graph that illustrate example gene profiling data for multiple mouse models for prostate cancer, according to an embodiment. The diagram groups the mouse models by phenotype listed above. The graph plots the t-SNE analysis showing relative distribution of the GEMMs. More detail is set forth in Example 2.

To generate a sufficient number of samples, while further increasing the variability of the corresponding expression profiles, a controlled set of exogenous perturbations was introduced by in vivo administration of 13 different small-molecule perturbagens to each GEMM. Perturbagens were selected for their clinical relevance and/or ability to modulate key prostate cancer pathways, including: hormone signaling (testosterone, calcitriol, or enzalutamide); PI3 kinase activity (MK2206, LY294002, and rapamycin); MAP kinase activity (PD035901); tyrosine kinase activity (imatinib, dasatinib, and sorafenib); NFB signaling (BAY 11-7082); JAK/STAT activity (WP1066); and chemotherapy (docetaxel). Following pilot studies to define the appropriate dose and schedule that produced the broadest range of gene expression changes, a universal schedule was adopted of 1 treatment per day for 5 days with dosage determined independently for each perturbagen, as described below in an experimental procedures section.

The resulting dataset contained 384 gene expression profiles, corresponding to the 13 GEMMs each treated with the 13 perturbagens or vehicles. The t-SNE analysis revealed that the resulting mouse dataset represented an extensive range of gene expression variability, as requisite for ARACNe. Specifically, while expression profiles from the same GEMMs and perturbagens clustered together, suggesting their effect was highly replicable, the diverse GEMMs and perturbagens provided independent and highly effective axes of expression heterogeneity. FIG. 1C is a block diagram and graph that illustrate example effects on gene profiling data for mouse models in response to various perturbagens, according to an embodiment. The schematic diagram depicts perturbagens used to treat the GEMMs. The graph plots the t-SNE analysis showing the relative distribution of perturbagens for a representative GEMM (i.e., the NP model).

Regulatory networks (interactomes) for human and mouse prostate cancer were generated using the Algorithm for the Reconstruction of Accurate Cellular Networks. FIG. 2A is a block diagram and graph that illustrates example interactomes for human and mouse models with prostate cancer, according to an embodiment. The suitability of these mouse and human interactomes for cross-species interrogation was next evaluated by developing a novel computational approach to assess the global conservation of their transcriptional programs described in detail in Example 2. Notably, conserved transcriptional regulators included many genes known to play important roles in prostate cancer, such as AR, ETS1, ETV4, ETV5, STAT3, MYC, BRCA1, and NKX3.1. In particular, AR displayed extensive correlation of its transcriptional activity between the human and mouse interactomes, consistent with its known role as a key regulator of prostate development and prostate tumorigenesis

The Master Regulator Inference algorithm (MARINa) (Carro et al., 2010; Lefebvre et al., 2010) was used to infer candidate master regulators (MRs) that act individually or synergistically to drive malignant prostate cancer in the conserved interactomes. MARINa estimates differential activity (DA) based on enrichment (differential expression, DE) of their activated and repressed targets in the malignancy signature. More specifically, MARINa identified candidate MRs based on the concerted differential expression of their ARACNe-inferred targets (i.e., their differential activity, DA). Specifically, “activated” MRs have positively-regulated and repressed targets significantly enriched among upregulated and downregulated genes, respectively, while “repressed” MRs have the converse. To interrogate the human prostate cancer interactome, a gene signature was used representing prostate cancer malignancy from the Taylor dataset, which compares aggressive prostate tumors (Gleason score≧8 with rapid biochemical recurrence; sample size n=10) versus indolent ones (Gleason score 6 tumors with no biochemical recurrence; sample size n=39). The resulting independent lists of human and mouse MRs were then integrated to produce a ranked list of 20 conserved MRs, including 7 activated and 13 repressed (joint p-value: p≦0.0074 by Stouffer's method). Notably, these conserved MRs were more likely to be associated with disease outcome than the non-conserved ones, and were also more likely to be differentially expressed in aggressive prostate tumors (metastatic versus non-metastatic; 100% versus 60%). FIG. 3C is a table that illustrates example ranking of master regulators for their impact on prostate cancer by various available algorithms. Using the ARACNe method to analyze all possible pairs among the conserved activated MRs, the only pair that was found to be statistically significant was FOXM1 and CENPF. Both FOXM1 and CENPF were differentially co-expressed at significantly elevated levels in aggressive prostate tumors and were predicted to be significantly associated with disease outcome. Thus, subsequent analyses were focused on this pair of cross-species conserved, synergistic MRs.

3. Method of Diagnosis: FOXM1 and CENPF are Prognostic Biomarkers of Aggressive Prostate Cancer

Analysis of high-density tissue microarrays (TMAs) revealed that the coexpression of FOXM1 and CENPF constituted a highly informative biomarker of poor disease outcome. FIG. 5 is a table that illustrates example clinical datasets used to determine whether synergistic master regulators FOXM1 and CENPF are prognostic biomarkers of prostate cancer outcomes, according to an embodiment. The datasets are listed along the top row, with their use in this study grouped by primary dataset (Taylor et al., 2010); secondary datasets; RNA gene expression datasets (Sboner et al., 2010; Glinsky et al., 2004); and protein immunohistochemistry tissue microarray (TMA) datasets (outcome TMA from MSKCC, and Metastasis TMA from Michigan). The categories of data in each dataset are given by the rows, as applicable. One row breaks down the number of samples for each cell type; one row gives the median age of the subjects. The next rows give the Pathology T stage; the clinical T stage; the Pathology N stage; the Pathology Gleason score; the biopsy Gleason score, the survival index (SVI); the extracapsular extension percentage; the biochemical recurrence (BCR) median time in months; the median overall survival in months; and, the median time to metastasis in months.

Analysis of protein expression of FOXM1 and CENPF was performed using high-density tissue primary tumor microarray (TMAs) (Donovan et al., 2008) and a metastasis TMA (Shah et al., 2004). Available clinico-pathological features of these cohorts as well as independent human datasets used for clinical validation are summarized in the Table of FIG. 5.

In particular, a high-density TMA containing primary tumors from a large cohort of subjects (sample size n=916) that had undergone prostatectomy at Memorial Sloan-Kettering Cancer Center from 1985 to 2003 (Donovan et al., 2008) was analyzed. These cases have extensive clinical follow-up data for up to 20 years, including time to biochemical recurrence, prostate-cancer specific survival, and time to metastasis. A second TMA was evaluated from the rapid autopsy program at the University of Michigan containing prostate cancer metastases (sample size n=60), including 6 lung, 11 liver, 22 lymph node, and 14 other sites (Shah et al., 2004). Immunostaining for FOXM1 or CENPF was performed on adjacent sections of each TMA slide and staining intensity was evaluated (see experimental procedures section, below).

FIG. 6A is an image that illustrates example micrographs of FOXM1 and CENPF stained tissues showing enhanced concentrations of both in aggressive prostate cancer tumors compared to other prostate tumors, according to an embodiment. These micrographs are based on the MSKCC prostatectomy TMA; and, analysis revealed that FOXM1 and CENPF were over-expressed in 33% and 37% of all cases, respectively, (sample size n=821 informative cases) with a trend toward increased expression in tumors with higher Gleason scores. Spearman rank correlation coefficient of FOXM1 and CENPF protein expression levels was 0.57 with p value <2.2×10⁻¹⁶, indicating the coexpression relationship is highly significant.

FIG. 6B is an image that illustrates example micrographs of FOXM1- and CENPF-stained tissues showing enhanced concentrations of both in prostate cancer that metastasized to lung and liver tumors. These micrographs are based on the Michigan metastasis TMA; and, analysis revealed that FOXM1 and CENPF were coexpressed in most of the prostate cancer metastases (88% and 90%, respectively, sample size n=53 informative cases) at significantly elevated levels. Spearman rank correlation coefficient of FOXM1 and CENPF protein expression levels was 0.43 with p value <0.001, indicating the coexpression is significant

Thus, coexpression of FOXM1 and CENPF at above-threshold levels, particularly their nuclear colocalization, as described in more detail below, was well correlated in both the MSKCC prostatectomy TMA and the Michigan metastasis TMA. Additionally, both FOXM1 and CENPF were overexpressed at the mRNA level and their coexpression was well-correlated in advanced prostate cancer and metastases from independent cohorts of human prostate cancer.

To determine whether expression of FOXM1 and/or CENPF is associated with disease outcome on the MSKCC TMA, 4 groups of subjects were defined based on their expression levels: (i) low/normal expression of both FOXM1 and CENPF (sample size n=418); (ii) high expression of FOXM1 and low/normal expression of CENPF (sample size n=97); (iii) high expression of CENPF and low/normal expression of FOXM1 (sample size n=133); and (iv) high expression of both FOXM1 and CENPF (sample size n=173). FIG. 6C through FIG. 6E are graphs that illustrate example Kaplan-Meier survival analysis based on protein expression levels of FOXM1 and CENPF with respect to time to biochemical recurrence, time to prostate cancer-specific death, or time to metastatic progression, respectively, according to an embodiment.

Kaplan-Meier survival analysis of these subject groups revealed that those having elevated expression of both FOXM1 and CENPF were associated with the worst outcome with high significance (low values of p) for three independent clinical endpoints, namely, time to biochemical-free recurrence (p≦4.4×10-6), death due to prostate cancer (p≦5.9×10 9), and time to metastasis (p≦1.0×10-16). The p-values correspond to a log-rank test and indicate the statistical significance of the association with outcome for each indicated branch compared to control (i.e., subjects with low protein expression of both FOXM1 and CENPF). Notably, co-subcellular localization of FOXM1 and CENPF in prostate tumors was also associated with the worst outcome for all three independent clinical endpoints, as described in more detail below. In contrast, elevated expression of only FOXM1 or CENPF was either not significant or marginally significant for biochemical recurrence and prostate-specific survival (p≦0.053 and p≦0.011 for FOXM1, respectively; p≦0.078 and p≦0.402 for CENPF, respectively), and was 10 to 13 orders of magnitude less significant, respectively, than coexpression for time to metastasis (p≦0.001 for FOXM1 and p≦3.1×10⁻⁶ for CENPF, respectively).

Association of FOXM1 and CENPF with disease outcome was independently corroborated in two independent human prostate cancer datasets that had not been used for training purposes elsewhere in this study; namely, the Glinsky dataset, in which biochemical recurrence is the clinical endpoint (Glinsky et al., 2004), and the Sboner dataset, in which the clinical endpoint is prostate cancer-specific overall survival (Sboner et al., 2010). Using these independent cohorts, the mRNA expression levels of FOXM1 and CENPF was evaluated as well as their MARINa-inferred activity. Kaplan-Meier survival analysis was then performed on 4 subject groups: (i) those with low inferred activity or expression for FOXM1 and CENPF; (ii) those with high inferred activity or expression only for FOXM1; (iii) those with high inferred activity or expression only for CENPF; and (iv) those with high inferred activity or expression for both FOXM1 and CENPF. FIG. 6F and FIG. 6G are graphs that illustrate example Kaplan-Meier survival analysis based on the interactome-inferred activity levels of FOXM1 and CENPF with respect to time to biochemical recurrence, or time to prostate cancer-specific death, respectively, according to an embodiment.

Similar to the analysis of protein expression on the TMA, subjects with high inferred activity or mRNA expression for both CENPF and FOXM1 were associated with the worst outcome in both cohorts, as measured by biochemical recurrence (p<6.5×10⁵) and prostate cancer-specific survival (p≦4.0×10⁵). The ARACNe-inferred activities levels were assessed for each subject sample in both cohorts. The p-values correspond to a log-rank test and indicate the statistical significance of the association with outcome for each indicated branch compared to control (i.e., subjects with low activity levels of both FOXM1 and CENPF). Notably, these findings reveal that their ARACNe-inferred activities are well-correlated with the actual expression of FOXM1 and CENPF proteins on the TMA, and further demonstrate the striking association of their co-expression/co-activity with poor disease outcome.

FIG. 7 is a table that illustrates example prognostic power of coexpression of protein levels of FOXM1 and CENPF, with death due to prostate cancer and time to metastasis as evaluation endpoints, according to an embodiment. C-statistics give the proportion of pairs in which the predicted event probability (e.g., probability of survival from prostate cancer) is higher for the subject who experienced the event of interest (e.g., coexpression of FOXM1 and CENPF) than that of the subject who did not experience the event. Analysis of coexpression of FOXM1 and CENPF on the MSKCC prostatectomy TMA using C-statistics revealed their robust prognostic value for disease-specific survival (C=0.71; confidence interval=0.59-0.84, p≦2.4×10-4), as well as time to metastasis (C=0.77; confidence interval=0.71-0.83, p≦3.0×10-19). Notably, coexpression of FOXM1 and CENPF proteins as diagnostic markers of aggressive prostate cancer dramatically improved the prognostic value compared to Gleason score alone, for both disease-specific survival (C=0.86; confidence interval=. 0.80-0.93, p≦1.0×10⁻³⁰; p value for improvement, p≦2.0×10⁻⁴) and time to metastasis (C=0.86; confidence interval=0.81-0.89, p≦6.5×10⁻⁵⁸; p value for improvement, p≦5.3×10⁻¹³). In certain embodiments of the invention, diagnosis of aggressive prostate cancer further includes determining, in addition to elevated coexpression of both FOXM1 and CENPF, high Gleason scores of score ≧8.

Taken together, these analyses of independent clinical cohorts using distinct statistical models demonstrate that elevated levels of coexpression of FOXM1 and CENPF is a good predictor of disease outcome. In an embodiment FOXM1 and CENPF are prognostic for aggressive prostate cancer or of prostate cancer progressing to an aggressive form when they are coexpressed at elevated levels of at least 35% compared to the levels expressed in control prostate tissue. Based on the results, certain embodiments are directed to a method for diagnosing aggressive prostate cancer or of identifying subjects with prostate cancer that is at high risk of progressing to an aggressive form by (a) obtaining a test prostate cancer sample from a subject having prostate cancer, and a control prostate tissue sample, (b) determining a level of expression of the prognostic genes (FOXM1) Forkhead box protein M1 and Centromere protein F (CENPF) in the test and control samples, (c) comparing the level of expression of prognostic genes FOXM1 and CENPF in the test sample to the corresponding level in the control sample, and (d) if the level of expression of both of the prognostic genes FOXM1 and CENPF in the test sample is at least 35% higher than the corresponding level in the control sample, then determining that the subject has an aggressive form of prostate cancer or is at high risk of developing an aggressive form of prostate cancer.

In certain embodiments the level of expression of FOXM1 and CENPF is determined by the level of mRNA encoding FOXM1 and CENPF, respectively; or by the level of FOXM1 protein and CENPF protein in the sample or combinations thereof. In another embodiment, a diagnosis of aggressive prostate cancer is reached by (a) obtaining a prostate cancer sample from a subject having prostate cancer, (b) determining a level of expression of FOXM1 protein and CENPF protein expression in the cancer cells in the sample by immunostaining with a first antibody that specifically binds to FOXM1 and a second antibody that specifically binds to CENPF, and (c) diagnosing aggressive prostate cancer if at least 50% of the cells in the test sample express both FOXM1 protein and CENPF protein at a composite score of at least 100 for each protein, wherein the composite score is calculated by multiplying the percent staining value by the staining intensity value. Any other method for determining that at least 50% of the cells in a prostate cancer sample coexpress both FOXM1 and CENPF proteins at levels of at least 35% above levels in control prostate tissue can be used, these include flow cytometry with differential florescent labeling of both proteins.

FIG. 8 is a flow chart that illustrates an example diagnostic method 800 for determining whether a subject has or is at high risk of undergoing a specific phenotypic transition based on coexpression of at least two synergistic master regulators, such as FOXM1 and CENPF for aggressive prostate cancer, according to an embodiment. Although steps are depicted in FIG. 8, and in subsequent flowchart FIG. 10, as integral steps in a particular order for purposes of illustration, in other embodiments, one or more steps, or portions thereof, are performed in a different order, or overlapping in time, in series or in parallel, or are omitted, or one or more additional steps are added, or the method is changed in some combination of ways.

In step 810, a subject is identified who has or is at high risk of producing the phenotype transition of interest, here development of aggressive prostate cancer from a prostate tumor or nodule detected in a subject. In step 803 a sample is taken from the identified subject, such as a biopsy of the prostate tumor or nodule. Biological samples for use in the present embodiments also include circulating prostate cancer cells or prostate tumor cells which can be detected using a variety of methods known in the art that select cells based on surface markers for example using antibodies against the surface markers, or expression of other prostate cancer markers. In some embodiments the prostate cancer cells can be selected by size. Biological samples for use in the present embodiments also include exosomes derived from prostate cancer cells, which are cell-derived vesicles that are present in many and perhaps all biological fluids, including blood. The reported diameter of exosomes is between 30 and 100 nm.

In step 805, the pattern of coexpression of synergistic master regulators, such as FOXM1 and CENPF, for the phenotype transition, such as to aggressive prostate cancer, is determined. For example, the pattern of certain genes' expression is determined by determining the relative level of coexpression of mRNA coding for the master regulators, or the intensity of immunostaining of polypeptides encoded by the master regulators, or the enhancement or deficiency of common targets of the master regulators, the latter by either mRNA levels or immunostaining intensities of polypeptides included. Step 805 is described in more detail below with reference to FIG. 10.

In step 807, it is determined whether the synergistic master regulators are coexpressed at significantly elevated (or reduced) levels above (below) some threshold level, or otherwise have different patterns than, determined in control prostate tissue. For diagnosis of aggressive prostate cancer or the risk of a tumor progressing to an aggressive form, it is determined whether FOXM1 and CENPF levels are both above corresponding threshold control levels, which are the levels seen in normal prostate tissue or indolent prostate cancer tumors. The threshold or pattern depends on the measurement type as described in more detail below with reference to FIG. 10.

If it is determined in step 807, that the synergistic master regulators are coexpressed at some elevated (or reduced) level or other different pattern, then control passes to step 811. Otherwise control passes to step 821.

In step 811, it is determined that the subject is at risk for developing the phenotype transition, or in fact is undergoing, or has undergone, the phenotype transition. In some embodiments the phenotype transition is to aggressive prostate cancer. In some embodiments, the risk is quantified based, at least in part, on the levels of coexpression of the synergistic master regulators. For example, the Gleason score is combined with the fact of elevated coexpression of FOXM1 and CENPF, to predict the risk of aggressive prostate cancer in the subject, as indicated by the table of FIG. 7. Control then passes to step 817 to treat the subject based on this risk or diagnosis.

In step 821, it is determined that the subject does not have or is at low risk or no risk for developing the phenotype transition, e.g., aggressive prostate cancer; and, the process ends, or is repeated with the same subject at a later time or with another subject.

More information on the secondary effects of elevated coexpression of FOXM1 and CENPF was obtained by experiments that were performed to validate synergistic interactions of master regulators and elucidate underlying mechanisms, as well as to evaluate their relevance for clinical outcome. FIG. 9A is a graph shows relative mRNA expression levels for the indicated genes in the indicated cell lines following individual or co-silencing (i.e., silencing both) of FOXM1 and CENPF. The p-values (indicated by one or two *) show the significance of the predicted additive effect versus actual observed effect on gene expression (*=p<0.01; **=p<0.001). Silencing was performed using lentivirus vectors for shRNA for each or both of the two genes FOXM1 and CENPF, as described in more detail below. The ARACNe-inferred common target genes include BRCA1, BUB1, KI67, CYCLIN A, TIMELESS, CDC25, TRIP13, PLK1, HHMR, MYBL2, BIRC5, AURKA, AURKB.

Although target gene expression was somewhat reduced by their individual silencing, as shown in FIG. 9A, co-silencing of FOXM1 and CENPF produced a significantly greater reduction for the majority of targets, consistent with the synergistic regulation of target gene expression by FOXM1 and CENPF. Notably, these findings were observed in each cell line that express both FOXM1 and CENPF, but not in LNCaP cells which do not express CENPF.

In addition, analyses of genomic binding of FOXM1 to its known target sites using chromatin immunoprecipitation (ChIP) was followed by quantitative PCR analyses. FIG. 9B is a graph that illustrates example enrichment of FOXM1 binding normalized to input with and without silencing of CENPF, according to an embodiment. Cells were infected with a lentivirus expressing a V5-tagged FOXM1 plus shRNA CENPF (or a control) and ChIP was done using an anti-V5 antibody. Data are expressed as fold of enrichment of FOXM1 binding normalized to input. This revealed that FOXM1 binding to its targets was abrogated by silencing CENPF, therefore suggesting that CENPF is required for appropriate genomic binding by FOXM1.

Interestingly, although a direct protein-protein interaction of FOXM1 and CENPF in co-immunoprecipitation assays was not observed, it was observed that FOXM1 and CENPF were co-localized in the nucleus of prostate cancer cells and that their subcellular colocalization was mutually dependent. FIG. 9C is an image of micrographs that illustrate example changes in subcellular localization of FOXM1 and CENPF proteins in prostate cancer cells after silencing either, according to an embodiment. Shown are microphotographs of immunofluorescence staining for FOXM1 or CENPF in the control or silenced cells as indicated. Arrows indicate subcellular localization or the shift in localization following silencing.

In particular, silencing of CENPF resulted in the redistribution of FOXM1 to the cytoplasm as well the nucleus, and conversely silencing of FOXM1 resulted in the accumulation of CENPF at the nuclear periphery. Notably, subcellular co-localization of FOXM1 and CENPF was also observed in human prostate tumors and associated with disease outcome. Taken together, these findings show that FOXM1 and CENPF synergistically regulate expression of mutual target genes, which mediated in part through their subcellular colocalization in prostate cancer cells.

Determining Coexpression of the Synergistic Master Regulators FOXM1 and CENPF

FIG. 10 is a flow chart that illustrates an example method 1000 for determining coexpression of the synergistic master regulators such as FOXM1 and CENPF, according to an embodiment. Method 1000 is a particular embodiment of step 805, described above. In step 1051 it is determined whether to use expression of the genes for the synergistic master regulators, or expression of the master regulator proteins (e.g., polypeptides included), or expression of the genes or polypeptides of one or more the targets in the signaling pathways of the master regulators, or combinations thereof. In the illustrated embodiment, it is assumed that expression of one or more targets is not used in the method 1000.

In step 1053, it is determined whether the gene expression or polypeptide expression is to be evaluated. If the gene expression is to be determined, control passes to step 1061. Otherwise control passes to step 1071.

In step 1061, the normalized level of mRNA is determined for FOXM1 and CENPF in the prostate sample. Certain methods and primers for determining the relative or normalized levels of mRNA for FOXM1 and CENPF compared to other genes are also described in the experimental procedures section, below, with primer sequences listed in Table 1 in that later section. In an example, total RNA was isolated from a subject sample of prostate tissues/tumors using a MagMAX-96 total RNA isolation kit and biotin-labeled using the Illumina TotalPrep RNA Amplification Kit (Life Technologies). Slides were scanned using an iScan (Illumina) and the resulting files were uploaded and background-corrected in BeadStudio 3.1.3.0 (Illumina, Inc.). Expression profiling data were normalized using standard variance stabilizing transformation (VST) and robust spline normalization (RSN) with lumiT and lumiN functions from lumi library, in R-system v2.14.0 (The R Foundation for Statistical Computing, ISBN 3-900051-07-0.)

In step 1063, the threshold for significantly elevated coexpression is determined, e.g., retrieved from data storage. An mRNA level in the subject prostate cancer sample that is at least 35% higher than the level expressed in normal prostate tissue for each gene is considered elevated. In other embodiments other thresholds are used. In some embodiments, the threshold for each to be considered elevated is selected in a range from about 35% to about 100% or more. In some embodiments the threshold is at least 50%; and in other embodiments the threshold is at least 75%. Control then passes to step 807 of FIG. 8, described above, to determine if the measured level exceeds the threshold.

In step 1071, the level of immunostaining is determined for FOXM1 and CENPF proteins. Certain antibodies for immunostaining FOXM1 and CENPF are identified in the experimental procedures section below and listed in Table 2, and procedures for quantifying the intensity levels are also described. Any antibody that selectively binds to either FOXM1 or CENPF can be used. Protein levels were determined by percent of staining (e.g., from 0 to 100%) and intensity level of staining (e.g., 0, 1, 2, or 3) in each tumor sample. A composite protein level is determined by multiplying percent of staining and its intensity level for each tumor sample, for FOXM1 or CENPF. In some embodiments, step 1071 includes determining the relative amounts of FOXM1 and CENPF inside the membrane of the nucleus of the cells where the staining is observed in the top row of FIG. 9C when both FOXM1 and CENPF are expressed. In various embodiments, this determination of the relative amount within the nucleus is done in addition to, or instead of, determining the composite protein level.

In step 1073, the threshold for elevated coexpression is determined, e.g., retrieved from data storage. Composite protein level exceeding 100 for each protein was considered elevated. Thus, in some embodiments, FOXM1 and CENPF are considered to be co-expressed if the determined composite protein level in the subject prostate tumor sample for each is above about 100.

In some embodiments, the pattern of coexpression is determined by the relative amount of the total FOXM1 and CENPF that is inside the same cell, or in a particular subcellular compartment, such as inside of the nuclear membrane. For example, if at least 50% of the cells in the test sample express both FOXM1 protein and CENPF protein at a composite score of at least 100 for each protein, then determining that coexpression is elevated.

Control then passes to step 807 of FIG. 8, described above, to determine if the measured level exceeds the threshold.

Method for Detecting mRNA Expression

In some embodiments, the methods described herein comprise detecting the presence of FOXM1 or CENPF RNA expression (e.g. mRNA expression), including detecting of the absolute or relative quantity of the RNA, the half-life of the RNA, a splicing or processing of the RNA, the nuclear export of the RNA or the sub-cellular location of the RNA. Such detection can be by various techniques known in the art, including by sequencing all or part of the FOXM1 or CENPF RNA or by selective hybridization or selective amplification of all or part of the FOXM1 or CENPF RNA. As described herein, there exist many suitable methods for detecting the presence and level of a nucleic acid encoding a FOXM1 polypeptide or a CENPF polypeptide, including, but not limited to genotyping a sample, for example via gene sequencing, selective hybridization, amplification, gene expression analysis (e.g. microarray analysis), oligonucleotide ligation assay, a confirmation based assay, a hybridization assay, a sequencing assay, an allele-specific amplification assay, a microsequencing assay, a melting curve analysis, a denaturing high performance liquid chromatography (DHPLC) assay (for example, see Jones et al, 2000), or a combination thereof. Sequencing can be carried out using techniques well known in the art, using automatic sequencers. The sequencing can be performed on the complete gene or on specific domains thereof, such as those known or suspected to carry deleterious mutations or other alterations. Other suitable methods include allele-specific oligonucleotide (ASO), oligonucleotide ligation, allele-specific amplification, Southern blot (for DNAs), Northern blot (for RNAs), single-stranded conformation analysis (SSCA), PFGE, fluorescent in situ hybridization (FISH), gel migration, clamped denaturing gel electrophoresis, denaturing HLPC, melting curve analysis, heteroduplex analysis, RNase protection, chemical or enzymatic mismatch cleavage, ELISA, radio-immunoassays (RIA) and immuno-enzymatic assays (IEMA). Some other approaches are based on specific hybridization between nucleic acids from the subject and a probe specific for wild type gene or RNA. The probe can be in suspension or immobilized on a substrate. The probe can be labeled to facilitate detection of hybrids. Some of these approaches are suited for assessing a polypeptide sequence or expression level, such as Northern blot, ELISA and RIA. These latter require the use of a ligand-specific for the polypeptide, for example, the use of a specific antibody.

In certain embodiments, detection or quantification of a nucleic acid encoding a nucleic acid encoding a FOXM1 polypeptide or a CENPF polypeptide (or a fragment thereof) can be by hybridization based methods. In certain embodiments, hybridization-based detection methods can employ a step of forming specific hybrids between complementary nucleic acid sequences that serve to detect nucleic acid sequences. Microarrays are a suitable hybridization based detection technique that can be used in connection with the methods described herein. Microarrays employ nucleic acid probes specific for wild type gene or RNA and can be used to investigate the expression of a nucleic acid encoding a FOXM1 polypeptide or a CENPF polypeptide in samples from patients in a diagnostic context. In general, microarrays comprise a two dimensional arrangement of nucleic acid or polypeptide probes which comprises an intentionally created collection of nucleic acid or polypeptide probes of any length spotted onto a substrate/solid support. The array itself can have different formats, e.g. libraries of soluble probes or libraries of probes tethered to resin beads, silica chips, or other solid supports. The process of microarray fabrication is well-known to the person skilled in the art. The process can comprise preparing a glass (or other) slide (e.g. chemical treatment of the glass to enhance binding of the nucleic acid probes to the glass surface), obtaining DNA sequences representing genes of a genome of interest, and spotting sequences these sequences of interest onto glass slide. Sequences of interest can be obtained via creating a cDNA library from an mRNA source or by using publicly available databases, such as GeneBank, to annotate the sequence information of custom cDNA libraries or to identify cDNA clones from previously prepared libraries. Generally, it is recommendable to amplify obtained sequences by PCR in order to have sufficient amounts of DNA to print on the array. The liquid containing the amplified probes can be deposited on the array by using a set of microspotting pins. Ideally, the amount deposited should be uniform. The process can further include UV-crosslinking in order to enhance immobilization of the probes on the array. Microarray chips suitable for use with the methods described herein are well known to those of skill in the art (see, e.g., U.S. Pat. Nos. 6,308,170; 6,183,698; 6,306,643; 6,297,018; 6,287,850; 6,291,183, each incorporated herein by reference). These are exemplary patents that disclose nucleic acid microarrays and those of skill in the art are aware of numerous other methods and compositions for producing microarrays. A microarray composition of the present invention can be employed for the diagnosis and treatment of any condition or disease in which the expression of FOXM1 and/or CENPF is implicated. The microarray-based methods can be used for large scale genetic or gene expression analysis of a large number of target sequences, including nucleic acids encoding a FOXM1 polypeptide or nucleic acids encoding a CENPF polypeptide. The microarray can also be used in the diagnosis of diseases and in the monitoring of treatments. Further, microarrays can also be employed to investigate an individual's predisposition to a disease. Furthermore, the microarrays can be employed to investigate cellular responses to infection, drug treatment, and the like.

When microarrays are used in connection with the methods described herein, the formation of a plurality of detectable complexes between probes and target nucleic acid sequences can be assessed. The expression profiles can show unique expression patterns that are characteristic of the presence or absence of a disease or condition, such as a malignant prostate cancer. In certain embodiments where expression profiles are examined using microarray technology, complexes can be formed by hybridization of one or more probes having complementarity to a nucleic acid encoding a FOXM1 polypeptide or a nucleic acid encoding a CENPF polypeptide. Such a microarray can be employed in several applications including diagnostics, prognostics and treatment regimens, drug discovery and development, toxicological and carcinogenicity studies, forensics, pharmacogenomics, and the like. The probe can be in suspension or immobilized on a substrate or support (for example, as in nucleic acid array or chips technologies). For example, a sample from the subject can be contacted with a nucleic acid probe specific for a nucleic acid encoding a FOXM1 polypeptide or a nucleic acid encoding CENPF polypeptide.

In certain embodiments, the expression profile can be used to a nucleic acid encoding a FOXM1 polypeptide or a nucleic acid encoding CENPF polypeptide infer changes in the expression of target genes implicated in disease wherein the expression of such target genes is upregulated or downregulated by FOXM1, CENPF, or by the concerted action of FOXM1 and CENPF. Example probes and primers useful for obtaining gene expression profiles in normal and malignant cells, and for comparing the gene expression in malignant and corresponding normal cells, are known in the art (Okabe et al., 2001; Kitahara et al., 2001; Lin et al., 2002; Hasegawa et al., 2002).

In certain embodiments, microarray-based detection and/or quantification of a nucleic acid encoding FOXM1 polypeptide and/or a nucleic acid encoding or a CENPF polypeptide can comprise steps of providing a biological sample from a person suspected of having a cancer (e.g. a malignant prostate cancer), and determining the level of expression of a nucleic acid encoding FOXM1 polypeptide and/or a nucleic acid encoding or a CENPF polypeptide in the cells of the biological sample. In particular, such embodiments of the methods described herein can comprises comprising the following steps: (a) contacting a cell sample nucleic acid with a microarray under conditions suitable for hybridization; (b) providing hybridization conditions suitable for hybrid formation between the cell sample nucleic acid and a polynucleotide of the microarray; (c) detecting the hybridization; and (d) diagnosing the disorder condition based on the results of detecting the hybridization.

For example, methods of purification of nucleic acids are described in Tijssen and van der Vliet, Laboratory Techniques in Biochemistry and Molecular Biology: Hybridization With Nucleic Acid Probes, Part I. Theory and Nucleic Acid Preparation, Elsevier, New York, 1993. In one case, total RNA is isolated using the TRIZOL reagent (Life Technologies, Gaithersburg Md.), and mRNA is isolated using oligo d (T) column chromatography or glass beads. Alternatively, when target polynucleotides are derived from an mRNA, the target polynucleotides can be a cDNA reverse transcribed from an mRNA, an RNA transcribed from that cDNA, a DNA amplified from that cDNA, an RNA transcribed from the amplified DNA, and the like. When the target polynucleotide is derived from DNA, the target polynucleotide can be DNA amplified from DNA or RNA reverse transcribed from DNA. In yet another alternative, the targets are target polynucleotides prepared by more than one method.

When target polynucleotides are amplified, it is desirable to amplify the nucleic acid sample and maintain the relative abundances of the original sample, including low abundance transcripts. Total mRNA can be amplified by reverse transcription using a reverse transcriptase and a primer consisting of oligo d(T) and a sequence encoding the phage T7 promoter to provide a single stranded DNA template. The second DNA strand is polymerized using a DNA polymerase and a RNAse which assists in breaking up the DNA/RNA hybrid. After synthesis of the double stranded DNA, T7 RNA polymerase can be added, and RNA transcribed from the second DNA strand template (Van Gelder et al., U.S. Pat. No. 5,545,522). RNA can be amplified in vitro, in situ or in vivo (see Eberwine, U.S. Pat. No. 5,514,545).

The sequence of the probes and primers suitable for use with hybridization or amplification based detection methods described herein can be derived from the sequences of a nucleic acid encoding a FOXM1 polypeptide or a CENPF polypeptide. According to the invention, a probe can be a polynucleotide sequence which is complementary to and specifically hybridizes with a, or a target portion of a nucleic acid encoding a FOXM1 polypeptide or a CENPF polypeptide, such as a DNA or RNA molecule encoding such polypeptides. Probes and primers suitable for use with the methods described herein include those that are complementary to a nucleic acid encoding a FOXM1 polypeptide or a CENPF polypeptide, can comprise single-stranded nucleic acids of between 8 to 1000 nucleotides in length, for instance between 10 and 800, between 15 and 700, or between 20 and 500. Exemplary probes and primers may be 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or more 100 nucleotides in length. In one embodiment, a useful probe or primers of the invention is a single stranded nucleic acid molecule of between 8 to 500 nucleotides in length, which can specifically hybridize to a region of a nucleic acid encoding a FOXM1 polypeptide or a CENPF polypeptide. Longer polynucleotides encoding 250, 500, or 1000 bases and longer are contemplated as well. Such oligonucleotides will find use, for example, as probes in Southern and Northern blots and as primers in amplification reactions.

Conditions can be selected for hybridization where an exactly complementary target and probes can hybridize, i.e., each base pair must interact with its complementary base pair. Alternatively, conditions can be selected where a target and probes have mismatches but are still able to hybridize. Suitable conditions can be selected, for example, by varying the concentrations of salt in the prehybridization, hybridization and wash solutions, by varying the hybridization and wash temperatures, or by varying the polarity of the prehybridization, hybridization or wash solutions.

Suitable hybridization conditions for the diagnostic methods are those conditions that allow the detection of gene expression from identifiable expression units such as genes. Exemplary stringent hybridization conditions include but are not limited to hybridization at 42° C. in a solution (i.e., a hybridization solution) comprising 50% formamide, 1% SDS, 1 M NaCl, 10% dextran sulfate, and washing twice for 30 minutes at 60° C. in a wash solution comprising 0.1×SSC and 1% SDS. Hybridization can be performed at low stringency with buffers, such as 6×SSPE with 0.005% Triton X-100 at 37° C., which permits hybridization between target and probes that contain some mismatches to form target polynucleotide/probe complexes. Subsequent washes are performed at higher stringency with buffers, such as 0.5×SSPE with 0.005% Triton X-100 at 50° C., to retain hybridization of only those target/probe complexes that contain exactly complementary sequences. Alternatively, hybridization can be performed with buffers, such as 5×SSC/0.2% SDS at 60° C. and washes are performed in 2×SSC/0.2% SDS and then in 0.1×SSC. Background signals can be reduced by the use of detergent, such as sodium dodecyl sulfate, Sarcosyl or Triton X-100, or a blocking agent, such as salmon sperm DNA. It is understood in the art that conditions of stringency can be achieved through variation of temperature and buffer, or salt concentration, as described in Ausubel, et al. eds., Protocols in Molecular Biology, John Wiley & Sons (1994), pp. 6.0.3 to 6.4.10. After hybridization, the microarray can be washed to remove nonhybridized nucleic acids, and complex formation between the hybridizable array elements and the target polynucleotides is detected. Modifications in hybridization conditions can be empirically determined or precisely calculated based on the length and the percentage of guanosine/cytosine (GC) base pairing of the probe. The hybridization conditions can be calculated as described in Sambrook, et al. eds., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y. (1989), pp. 9.47 to 9.51.

Detection of hybridization can be achieved by labelling probes or target polynucleotides (e.g. a nucleic acid encoding a FOXM1 polypeptide or a nucleic acid encoding a CENPF polypeptide with one or more labeling moieties. In one embodiment, the target polynucleotides are labeled with a fluorescent label, and measurement of levels and patterns of fluorescence indicative of complex formation is accomplished by fluorescence microscopy (e.g. confocal fluorescence microscopy). The labeling moieties can include compositions that can be detected by spectroscopic, photochemical, biochemical, bioelectronic, immunochemical, electrical, optical or chemical means. The labeling moieties include radioisotopes, such as 3H, 14C, 32P, 33P or 35S, chemiluminescent compounds, labeled binding proteins, heavy metal atoms, spectroscopic markers, such as fluorescent markers and dyes, magnetic labels, linked enzymes, mass spectrometry tags, spin labels, electron transfer donors and acceptors, and the like. Exemplary dyes include quinoline dyes, triarylmethane dyes, phthaleins, azo dyes, cyanine dyes, and the like. Fluorescent markers that emit light at wavelengths at least greater than 10 nm above the wavelength of the light absorbed can be used in some embodiments. Exemplary fluorescent markers include, but are not limited to, fluorescein, phycoerythrin, rhodamine, lissamine, and C3 and C5 available from Amersham Pharmacia Biotech (Piscataway N.J.). Labeling can also be carried out during an amplification reaction, such as polymerase chain reactions and in vitro transcription reactions, or by nick translation or 5′ or 3′-end-labeling reactions. When the label may be incorporated after or without an amplification step, the label is incorporated by using terminal transferase or by phosphorylating the 5′ end of the target polynucleotide using, e.g., a kinase and then incubating overnight with a labeled oligonucleotide in the presence of T4 RNA ligase. Alternatively, the labeling moiety can be incorporated after hybridization once a probe/target complex has formed. Nucleotide substitutions can be performed, as well as chemical modifications of the probe. Such chemical modifications can be accomplished to increase the stability of hybrids (e.g., intercalating groups) or to label the probe. Some examples of labels include, without limitation, radioactivity, fluorescence, luminescence, and enzymatic labeling.

In embodiments where amplification used to detect the presence of a nucleic acid encoding a FOXM1 polypeptide or nucleic acid encoding a CENPF polypeptide, such methods can be based on the formation of specific hybrids between primers nucleic acid sequences having complete or partial complementarity to portions of a nucleic acid encoding a FOXM1 polypeptide or to portions of a nucleic acid encoding a CENPF polypeptide, wherein the primer sequences serve to initiate nucleic acid reproduction though, for example, PCR based methodologies. Numerous nucleic acid amplification techniques known in the art, including traditional polymerase chain reaction (PCR), quantitative PCR (qPCR), ligase chain reaction (LCR), strand displacement amplification (SDA) and nucleic acid sequence based amplification (NASBA). These techniques can be performed using commercially available reagents and protocols. Useful techniques in the art encompass real-time PCR, allele-specific PCR, or PCR-SSCP. Nucleic acid primers useful for amplifying a nucleic acid encoding a FOXM1 polypeptide or nucleic acid encoding a CENPF polypeptide include, but are not limited to primers that specifically hybridize with a DNA encoding a FOXM1 polypeptide or nucleic acid encoding a CENPF polypeptide, or an RNA encoding a FOXM1 polypeptide or nucleic acid encoding a CENPF polypeptide.

In some embodiments, the detection is performed by sequencing all or part of a nucleic acid encoding a FOXM1 polypeptide or a CENPF polypeptide or by selective hybridization or amplification of all or part of a nucleic acid encoding a FOXM1 polypeptide or a CENPF polypeptide. In one embodiment, the sample can comprise prostate tissue sample from a subject.

Thus, in certain aspects, the diagnostic methods described herein comprise the use of a nucleic acid primer, wherein the primer can be complementary to and hybridize specifically to a portion of a coding sequence (e.g., gene or RNA) of a nucleic acid encoding FOXM1 or CENPF present in a sample form a subject having or at risk of developing a cancer, such as a prostate cancer, or a malignant prostate cancer. Primers suitable for use with the methods described herein include those that are specific for a nucleic acid encoding FOXM1 or CENPF. By using such primers, the detection of an amplification product indicates the presence of a nucleic acid encoding FOXM1 or CENPF or the absence of such. The use of such primers can also be employed to quantify the relative or absolute amount of a nucleic acid encoding FOXM1 or CENPF in a sample.

Primers suitable for use with the methods described herein, include, but are not limited to those having the sequence of SEQ ID NOs: 5, 6, 19 and 20. In certain embodiments, amplification of a FOXM1 nucleic acid sequence can be performed using a primer pair of SEQ ID NO: 5 and 19. In certain embodiments, amplification of a CENPF nucleic acid sequence can be performed using a primer pair of SEQ ID NO: 6 and 20. One of skill in the art will readily be able to design and synthesize primers suitable for amplifying FOXM1 or CENPF nucleic acid sequences.

Examples of primers of this invention can be single-stranded nucleic acid molecules of about 5 to 100 nucleotides in length, or about 8 to about 25 nucleotides in length. Exemplary primers may be 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more contiguous base pairs from the above sequences will be used, although others are contemplated. Primers suitable for use with the methods described herein can be labelled according to any method known in the art, including those described for use in labeling the probes and oligonucleotides suitable for use with the methods described herein. Labelling of primers can also be limited to labelling methods that do not interfere with the ability of the primer to be used for amplification purposes.

The sequence of a primer suitable for use with the methods described herein can be derived directly from a nucleic acid encoding FOXM1 or CENPF. Perfect complementarity is useful, to ensure high specificity. However, certain mismatch can be tolerated. For example, a nucleic acid primer or a pair of nucleic acid primers as described herein can be used in a method for detecting the presence of or a predisposition to prostate cancer in a subject.

Amplification methods include, e.g., polymerase chain reaction, PCR (see Innis ed., 1990; and Innis ed., 1995); ligase chain reaction (LCR) (see, e.g., Wu, 1989; Landegren, 1988; Barringer, 1990); transcription amplification (see, e.g., Kwoh, 1989); self-sustained sequence replication (see, e.g., Guatelli, 1990); Q Beta replicase amplification (see, e.g., Smith, 1997), automated Q-beta replicase amplification assay (see, e.g., Burg, 1996) and other RNA polymerase mediated techniques (e.g., NASBA, Cangene, Mississauga, Ontario); see also Berger, 1987; Sambrook; Ausubel; U.S. Pat. Nos. 4,683,195 and 4,683,202; Sooknanan, 1995. All the references stated above are incorporated by reference in their entireties.

Methods for Determining Protein Expression

According to the methods described herein, the coexpression of FOXM1 and CENPF protein is defined as being elevated to a diagnostic level if the amount of FOXM1 polypeptide and CENPF polypeptide expressed or present in a sample exceeds a defined composite score threshold. For example, in certain embodiments, a sample can be deemed to have elevated expression of FOXM1 and CENPF by investigating immunochemical staining (e.g. immunochemical staining using antibodies specific to FOXM1 or CENPF) of a sample from a subject, determining the percentage of the sample that is stained and assigning a percent staining value for the sample between 0% and 100%, determining an intensity for the staining and assigning a staining intensity value for the sample on a scale of 0, 1, 2, or 3, and calculating a score by multiplying the percent staining value by the staining intensity value, wherein a score exceeding 100% indicates that the FOXM1 polypeptide and CENPF polypeptide present or expressed in the sample is at an elevated level. Thus, in certain aspects, the invention described herein related to the finding that a composite score based on (a) the percentage of a sample that is stained with immunochemical (e.g. an antibody, or a composition comprising an antibody), and (b) the intensity of the stain, can be used to diagnose a subject as having an aggressive or malignant prostate cancer, having a risk of dying from a prostate cancer, and having a risk of a prostate cancer undergoing metastasis. One of skill in the art will readily appreciate that the scoring scales described herein need not be limited to integers and may include fractional values. One of skill in the art will also understand that many variants of the composite scoring scale can be envisioned. For example, staining intensity can be ranked on a scale of 0 to 7 while retaining the fidelity of the method. Similarly, staining intensity can be ranked on a scale of 0 to 10 while retaining the fidelity of the system.

Detection of a polypeptide in accordance with the methods described herein can comprise detecting the presence of FOXM1 or CENPF polypeptide sequences in samples. In certain embodiments, detection of a polypeptide can comprise assaying for the presence of an elevated quantity FOXM1 or CENPF polypeptide in a subject prostate cancer sample as compared to a control (noncancerous) sample. In certain embodiments, detection of a polypeptide can comprise detecting the subcellular localization of a quantity FOXM1 or CENPF polypeptide, and/or detection of colocalization of FOXM1 and CENPF polypeptide within a cell.

A variety of methods may be used to measure FOXM1 or CENPF protein levels including, but not limited to, immunologically based methods such as standard ELISA, immuno-polymerase chain reaction (immuno-PCR) (Sano, 1992), immunodetection amplified by T7 RNA polymerase (IDAT) (Zhang, 2001), radioimmunoassay, immunoblotting, etc. Other approaches include two-dimensional gel electrophoresis, mass spectrometry, and proximity ligation (Fredriksson, 2002).

In embodiments where detection of FOXM1 and CENPF is at the level of polypeptide expression, different types of ligands can be used, such as antibodies that specifically recognize FOXM1 or CENPF polypeptides. Thus, in certain embodiments where the methods described herein involve detection of a FOXM1 or a CENPF polypeptide, a test sample can be contacted with an antibody specific for a FOXM1 or a CENPF polypeptide and the formation of an immune complex can be subsequently determined to determine the presence or location of the polypeptide. Various methods for detecting an immune complex can be used, such as ELISA, radioimmunoassays (RIA) and immuno-enzymatic assays (IEMA).

Antibodies suitable for use with the methods described herein can be polyclonal antibodies, a monoclonal antibodies, as well as fragments or derivatives thereof having substantially the same antigen specificity. Fragments of antibodies that are suitable for use with the methods described herein include Fab, Fab′2, or CDR regions. Derivatives of antibodies that are suitable for use with the methods described herein include single-chain antibodies, humanized antibodies, or poly-functional antibodies. An antibody specific for a FOXM1 polypeptide or a CENPF polypeptide can be an antibody that selectively binds to FOXM1 or CENPF, namely, an antibody raised against FOXM1 or CENPF polypeptide or an epitope-containing fragment of either polypeptide. Although non-specific binding towards other antigens can occur, binding to the target polypeptide occurs with a higher affinity and can be reliably discriminated from non-specific binding. One of skill in the art will appreciate that many methods exist for labelling antibodies for microscopic detection in samples. Exemplary labelling methods include, but are not limited fluorescent labeling, radioactive labeling, and quantum dots.

The diagnostic methods described herein can be performed on any suitable sample which contains nucleic acids or polypeptides, including in vitro, ex vivo, or in vivo samples. Examples of samples suitable for use with the methods described herein include prostate tissue samples, especially samples of prostate tumor or cancerous prostate cells from tissue biopsies taken from a subject having prostate cancer or at risk of developing it. In one embodiment, the sample comprises a tumor tissue. In one embodiment, the sample comprises prostate tissue. In another embodiment, the sample is an isolated population of prostate stem cells. The sample can be collected according to conventional techniques and used directly for diagnosis or stored. The sample can be treated prior to performing the method, in order to render or improve availability of nucleic acids or polypeptides for testing. Treatments include, for instance, lysis (e.g., mechanical, physical, or chemical), and centrifugation. Also, the nucleic acids and/or polypeptides can be pre-purified or enriched by conventional techniques, and/or reduced in complexity. Nucleic acids and polypeptides can also be treated with enzymes or other chemical or physical treatments to produce fragments thereof. In one embodiment, the sample is contacted with reagents, such as probes, primers, or ligands, in order to assess the presence of FOXM1 or CENPF polypeptides or nucleic acids. Contacting can be performed in any suitable device, such as a plate, tube, well, or glass. In specific embodiments, the contacting is performed on a substrate coated with the reagent, such as a nucleic acid array or a specific ligand array. The substrate can be a solid or semi-solid substrate such as any support comprising glass, plastic, nylon, paper, metal, or polymers. The substrate can be of various forms and sizes, such as a slide, a membrane, a bead, a column, or a gel. The contacting can be made under any condition suitable for a complex to be formed between the reagent and the nucleic acids or polypeptides of the sample.

Diagnostic Kits

The invention also provides for diagnostic kits comprising products and reagents for detecting in a sample from a subject the presence of a FOXM1 or CENPF polypeptides or nucleic acids or FOXM1 or CENPF activity. The kits can be useful for determining whether a sample from a subject expresses significantly elevated levels of FOXM1 or CENF compared to the level expressed in normal prostate tissue. For example, the diagnostic kit according to the present invention comprises any primer, any pair of primers, any nucleic acid probe and/or any ligand, suitable for use with the methods described herein. The diagnostic kits according to the present invention can further comprise reagents and/or protocols for performing a hybridization, amplification or antigen-antibody immune reaction. In certain embodiments, the kits can comprise nucleic acid primers that specifically hybridize to and can prime a polymerase reaction from a nucleic acid encoding FOXM1 or a nucleic acid encoding CENPF. In some kits nucleic acids that specifically hybridize to a nucleic acid encoding FOXM1 or a nucleic acid encoding CENPF wherein in an embodiment the nucleic acid is affixed to a microarray support.

Some kits include anti-FOXM1 and/or anti-CENPF antibodies or fragments thereof, including monoclonal and polyclonal antibodies, and secondary antibodies that are labeled for easy detection for example with a fluororphore or horseradish peroxidase enzyme. The labeling moieties can include compositions that can be detected by spectroscopic, photochemical, biochemical, bioelectronic, immunochemical, electrical, optical or chemical means as described herein. For example, in certain embodiments, elevated nuclear colocalization of FOXM1 and CENPF can be microscopic immunofluorescent colocalization, wherein the extent of colocalization of FOXM1 and CENPF is determined using a Pearson colocalization co-efficient, a Spearman colocalization coefficient, or the like. In certain embodiments, an amount of nuclear colocalization yielding a Spearman colocalization coefficient P value of less than about 1.3×10-11 indicates that the sample is from a subject having a prostate cancer that has undergone, or is at risk of undergoing metastasis. In certain embodiments, an amount of nuclear colocalization yielding a Spearman colocalization coefficient P value of less than about 6.2×10-10 indicates that the sample is from a subject having a prostate cancer that has undergone, or is at risk of undergoing metastasis. In certain embodiments, an amount of nuclear colocalization yielding a Spearman colocalization coefficient P value of less than about 2.2×10-6 indicates that the sample is from a subject at risk of dying from a prostate cancer. In certain embodiments, an amount of nuclear colocalization yielding a Spearman colocalization coefficient P value of less than about 3.5×10-5 indicates that the sample is from a subject at risk of dying from a prostate cancer.

4. Method of Treatment of Aggressive Prostate Cancer

Co-Silencing of FOXM1 and CENPF Abrogated of Colony Formation in Each Cell Line that Expresses Both FOXM1 and CENPF

It was discovered that silencing both FOXM1 and CENPF resulted in a dramatic reduction of prostate tumor weight and volume in vivo. To evaluate their functions and potential synergy in prostate cancer, FOXM1 and/or CENPF were silenced individually or together in four distinct human prostate cell lines, namely DU145, PC3, LNCaP and 22Rv1, which have differing tumorigenic properties and responses to androgen signaling (FIG. 5A). All of these cell lines express high levels of both FOXM1 and CENPF, with the exception of LNCaP cells that express FOXM1 but not CENPF (FIG. 5B), making LNCaP cells an excellent negative control for analysis of synergy. To silence FOXM1 and/or CENPF, doxycycline-inducible lentiviral vectors were engineered expressing shRNAs for FOXM1 or CENPF; alternatively a control shRNA was used. The co-silencing of FOXM1 and CENPF produced a significantly greater reduction for the majority of the targets of each gene than did silencing each gene individually, which is consistent with the synergistic regulation of target gene expression by FOXM1 and CENPF coexpression. These findings were observed in each cell line that express both FOXM1 and CENPF, but not in LNCaP cells which do not express CENPF.

FIG. 11A shows various protocols for silencing FOXM1 or CENPF expression using lentiviral silencing vectors expressing shRNA for FOXM1 or CENPF or both or a control vector lacking the FOXM1 or CENPF shRNA. Lentiviral silencing vectors expressing shRNA for FOXM1 and/or CENPF (or a control shRNA for no gene expressed with either an RFP (red) or GFP (green) reporter (i.e., a gene that codes for a red fluorescent protein, RFP, or green fluorescent protein, GFP), were introduced into human prostate cancer cells. Unless otherwise indicated, analyses were done using two independent shRNAs for each gene in each of four independent prostate cancer cell lines. FIG. 11B is an image of Western blots that illustrate effectiveness of lentiviral silencing vectors, according to an embodiment, by showing expression of FOXM1 or CENPF proteins in DU145 cells expressing the indicated shRNAs.

FIG. 11C is an image that illustrates that DU145 cell colonies, visualized using crystal violet, are drastically reduced by silencing both FOXM1 and CENPF compared to other combinations. FIG. 11D is graph illustrating that the quantitative number of DU145 cell colonies are drastically reduced by silencing both FOXM1 and CENPF compared to other combinations. Quantification of colonies was performed using ImageJ.

In these various analyses, “synergistic” versus “additive” effects of FOXM1 and CENPF are distinguished by first extrapolating their “predicted additivity” based on their individual silencing and then comparing this predicted value to their “actual” observed effect following their co-silencing. See the experimental procedures discussion in a later section. For any given assay, if the “predicted additive” is statistically different from the “actual,” it is concluded that FOXM1 and CENPF are synergistic rather than additive.

With respect to cellular proliferation depicted in FIG. 11C, individual silencing of FOXM1 and, to a lesser extent, CENPF resulted in reduced cell proliferation. However, the reduction following co-silencing was statistically greater (p<0.01; log linear model) than the “predicted additive” increase and therefore was synergistic for each cell line that expresses both FOXM1 and CENPF. Similarly, with respect to colony formation depicted in FIG. 11D, while individual silencing of FOXM1 or CENPF (Aytes et++al.) reduced the number of colonies, their co-silencing resulted in nearly complete abrogation of colony formation in each cell line that expresses both FOXM1 and CENPF (p<0.001; log linear model). Importantly, co-silencing of FOXM1 and CENPF was not associated with reduced viability, apoptosis, or further cell cycle arrest relative to their individual silencing, suggesting that their observed synergistic activities were not simply due to induction of cell death or secondary to cell cycle arrest.

Co-Silencing FOXM1 and CENPF Completely Abrogated Tumor Growth and Caused a Profound Reduction in Tumor Weight

To investigate their consequences of silencing FOXM1 and CENPF on prostate tumor growth in vivo, DU145 cells expressing silencing vectors for FOXM1 and/or CENPF (or controls) were engrafted into immunodeficient mice and prostate tumor growth was monitored in vivo. FIG. 11E is a block diagram illustrating an example in vivo experiment based on prostate tumor growth with silencing of either FOXM1 or CENPF or both. Beginning on day 7, mice were administered doxycycline to induce shRNA expression and tumor growth was monitored for one month. FIG. 11F shows that in vivo prostate tumor volume growth was dramatically reduced when both FOXM1 and CENPF were silenced, and this effect was more than additive of the effects of silencing either FOXM1 or CENPF separately. The dashed line shows the predicted additive effect of co-silencing FOXM1 and/or CENPF estimated using a log linear model; the p-value indicates the significance between the predicted additive versus and the actual observed consequences of co-silencing FOXM1 and CENPF. FIG. 11G shows that in vivo tumor weight at time of sacrifice was also dramatically reduced when both FOXM1 and CENPF were silenced compared to silencing either FOXM1 or CENPF separately. Associated p values indicate the difference between the predicted additive and the actual observed consequences of co-silencing FOXM1 and CENPF was significant and therefore that the results are synergistic. FIG. 11H shows micrographs of prostate tumors from several mice on identical distance scales in co-silenced FOXM1 and CENPF compared to silencing only one.

Consistent with the cell culture studies, individual silencing of FOXM1 or CENPF resulted in a modest but statistically significant reduction in tumor growth (2.0 fold, p≦2×10⁻³ and 1.5 fold, p≦2×10⁻³, respectively), as well as tumor weight (2.3 fold, p≦7×10-3, and 1.6 fold, p≦1×10⁻², respectively). However, co-silencing of FOXM1 and CENPF resulted in a complete abrogation of tumor growth (10.2 fold reduced, p≦1.3×10⁵) and profound reduction in tumor weight (12.9 fold, p≦1.1×10⁵). Notably, the actual observed inhibition of tumor growth following co-silencing FOXM1 and CENPF were significantly greater than their “predicted additive” reduction based on their individual silencing (3.3 fold difference, p<2.6×10⁻⁴; log-linear model) (see FIG. 11F), supporting the conclusion that FOXM1 and CENPF synergistically regulate tumor growth in vivo.

To further evaluate the synergistic activity of FOXM1 and CENPF for prostate tumor growth, an in vivo competition assay was developed. FIG. 11I shows an example in vivo competition assay in which equal numbers of DU145 cells expressing the control shRNA (control cells), or the experimental shRNA for FOXM1 or CENPF or both (experimental cells) as well as red or green reporters (RFP or GFP, respectively) were implanted into mouse hosts. Specifically, DU145 cells were infected with silencing vectors expressing an FOXM1 shRNA and an RFP reporter (R) or a CENPF shRNA and a GFP reporter (G), or both lentiviruses (resulting in yellow images, Y). As negative controls, DU145 cells were infected with control vectors lacking the FOXM1 or CENPF shRNA but expressing the fluorescent reporters. Equal numbers of viable red, green, or yellow cells from the experimental or control groups were then implanted into immunodeficient mice. Tumor growth in vivo was monitored for one month. Following the one month growth in vivo, tumors were collected and sorted by fluorescence-activated cell sorting (FACS) to quantify the total number of red, green, or yellow cells in individual tumors for control and experimental groups.

FIG. 11J and FIG. 11K provide example fluorescence-activated cell sorting (FACS) plots showing the percentage of red cells (R, FOXM1 silenced), green cells (G, CENPF silenced) or yellow cells (Y, both silenced) relative to the total number of fluorescent cells for control tumors and experimental tumors, respectively, according to an embodiment. FIG. 11L and FIG. 11M are graphs that illustrate example percentages of red, green or yellow cells relative to the total number of fluorescent cells for control tumors and experimental tumors, respectively, indicating profound selection against cells co-silenced for FOXM1 and CENPF.

Tumors derived from control cells (sample size n=4) were comprised of equivalent numbers of red (34%±0.6%), green (34%±2.7%) and yellow (33%±1.2%) cells, indicating that the respective lentiviral vectors offer no selective growth advantage (p≦0.614; Hotelling's one-sample T-squared test) (FIG. 11K through FIG. 11M). In striking contrast, tumors derived from the experimental cells (sample size n=7) were comprised primarily of green CENPF-silenced cells (57%±3.5%) and red FOXM1-silenced cells (41%±2.6%), while there were virtually no yellow, co-silenced cells (2.0%±0.3%). This profound selection against cells co-silenced for FOXM1 and CENPF was highly significant (p≦1×10⁻⁴; Hotelling's one-sample T-squared test) showing that tumor cells in which both genes are co-silenced do not survive. This further supports the conclusion that FOXM1 and CENPF synergistically regulate tumor growth in vivo.

To elucidate molecular pathways that underlie their synergistic interaction for prostate tumor growth, gene expression profiles from prostate cancer cells in which FOXM1 and/or CENPF were individually silenced or co-silenced were analyzed. Among the genes that were differentially expressed (relative to control cells) following individual silencing of FOXM1 or CENPF were a majority of their ARACNe-inferred targets (p≦0.0028 for enrichment of FOXM1 targets; p≦0.001 for enrichment of CENPF targets), further confirming the accuracy of the ARACNe analysis. Inspection of these target genes as well as gene set enrichment analysis (GSEA) of enriched biological pathways confirmed the known individual functions of FOXM1 and CENPF as regulators of cellular proliferation, reduction of stress response and/or regulation of mitosis.

Co-silencing of FOXM1 and CENPF also revealed a new repertoire of significantly differentially expressed genes and enriched biological pathways that had not been evident by their individual silencing. In particular, co-silencing of FOXM1 and CENPF revealed the enrichment of key biological pathways associated with tumorigenesis, including: “Cell cycle” (normalized enrichment score (NES) 1.32; p≦0.001), “stress pathway” (NES 1.58; p≦0.01), “regulation of insulin-like growth factor” (NES 1.89; p≦0.001), “signaling by NGF” (NES 1.25; p≦0.001), “Metabolism of amino acids” (NES 1.25; p≦0.01), “PI3-Akt signaling” (NES 1.89; p≦0.001), “MAP kinase pathway” (NES 1.34; p≦0.008), “Telomere maintenance” (NES 1.35; p≦0.01) and “Cell adhesion molecules” (NES 1.32; p≦0.001). Of particular interest was the enrichment of PI3-kinase and MAP kinase signaling pathways, which were enriched following co-silencing of FOXM1 and CENPF, as these constitute established hallmarks of aggressive prostate cancer (Aytes et al., 2013; Taylor et al., 2010).

FIG. 11N is an image of Western blots that illustrate example changes in expression of the indicated representative markers of the PI3-kinase and MAP kinase signaling pathways associated with tumor growth in DU145 and PC3 prostate cancer cells after silencing either FOXM1 or CENPF or both, according to an embodiment. As evident by this Western blot analysis, both pathways are completely abrogated following co-silencing of FOXM1 and CENPF showing that therapeutic targeting FOXM1 and CENPF in prostate cancer cells may be effective for inactivation of key signaling pathways such as PI3-kinase and MAP kinase.

Although the individual functions of FOXM1 and CENPF in cancer have been well-studied, the findings described here have uncovered their novel synergistic interaction in aggressive prostate cancer, which could not have been anticipated from their previous analyses. Cumulatively, the new findings show that coexpression of FOXM1 and CENPF in aggressive prostate cancer leads to co-regulation of transcriptional programs, which ultimately result in activation of the key signaling pathways associated with cancer malignancy, including activation of PI3K and MAPK signaling pathways.

Based on the described results, certain embodiments are directed to methods of slowing the progression of non-aggressive prostate cancer to an aggressive form, and for treating aggressive prostate cancer by administering therapeutically effective amounts of active agents to significantly reduce the expression of FOXM1 and CENPF; typically these are different agents. In various embodiments the therapeutic agents are inhibitory oligonucleotides including inter alia antisense, siRNA and shRNA, which reduce expression of the gene or mRNA encoding FOXM1 and CENPF, which agents are described in more detail below. FOXM1 and CENPF can also be targeted pharmacologically using for example non-oligonucleotides. Such agents that reduce CENPF expression include Rapamycin, mTOR inhibitors, PI3K inhibitors, MEK inhibitors, tyrosine kinase inhibitors, and AKT kinase inhibitors (Halasi and Gartel, 2013b; Pan and Yeung, 2005; Radhakrishnan et al., 2006).

mTOR inhibitors include Rapamycin, but deforolimus (AP23573, MK-8669), everolimus (RAD001), and temsirolimus (CCI-779) are the newly developed rapamycin analogs. Rapamycin analogs are small molecule inhibitors that have been evaluated as anticancer agents. The analogs are reported to have a more favorable pharmacokinetic profile compared to rapamycin, the parent drug, despite the same binding sites for mTOR and FKBP12. Rapamycin analog temsirolimus (CCI-779)] is also a noncytotoxic agent which delays tumor proliferation. The second generation of mTOR inhibitors, some of which are in clinical trials, are known as ATP-competitive mTOR kinase inhibitors. mTORC1/mTORC2 dual inhibitors are designed to compete with ATP in the catalytic site of mTOR. They inhibit all of the kinase-dependent functions of mTORC1 and mTORC2 and therefore, block the feedback activation of PI3K/AKT signaling, unlike analogs that only target mTORC1. They also decrease protein translation, attenuate cell cycle progression, and inhibit angiogenesis in many cancer cell lines and also in human cancer.

The close interaction of mTOR with the PI3K pathway has also led to the development of mTOR/PI3K dual inhibitors including NVP-BEZ235, BGT226, SF1126, PKI-587 and many more. Compared with drugs that inhibit either mTORC1 or PI3K, these drugs have the benefit of inhibiting mTORC1, mTORC2, and all the catalytic isoforms of PI3K. Targeting both kinases at the same time reduces the upregulation of PI3K, which is typically produced with an inhibition on mTORC1. mTORC1/mTORC2 dual inhibitors (TORCdIs) include INK128, AZD8055, and AZD2014.

MEK inhibitors are chemicals or drugs that inhibit the mitogen-activated protein kinase kinase enzymes MEK1 and/or MEK2 that affects the MAPK/ERK pathway, which is often overactive in some cancers. MEK inhibitors include Trametinib (GSK1120212), FDA-approved to treat BRAF-mutated melanoma; dabrafenib; Selumetinib, for use in treating non-small cell lung cancer (NSCLC); Binimetinib or MEK162, for treating biliary tract cancer and melanoma; PD-325901, for breast cancer, colon cancer, and melanoma; Cobimetinib or XL518, in combination with vemurafenib (Zelboraf(R)), for treatment of advanced melanoma; CI-1040; and PD035901.

Tyrosine kinase inhibitors include bosutinib (Bosulif); crizotinib (Xalkori); dasatinib Sprycel); erlotinib (Tarceva); imatinib (Gleevec); gefitinib; lapatinib (Tykerb); nilotinib (TasignaO; sorafenib (Nexavar); and sunitinib (Sutent). Tyrosine kinases are enzymes responsible for the activation of many proteins by signal transduction cascades by adding a phosphate group to the protein (phosphorylation).

P13K inhibitors include many commercially available molecules: BEZ235 (NVP-BEZ235, Dactolisib), Pictilisib (GDC-0941), LY294002 (the first synthetic molecule known to inhibitPI3K/6/(3), CAL-101 (Idelalisib, GS-1101) and many others available from Selleck/Pfeizer.

AKT Kinase inhibitors are also well known and include Perifosine (KRX-0401) is a novel Akt inhibitor, MK-2206 2HC1 is a highly selective inhibitor of Akt1/2/3,Miltefosine inhibits PI3K/Akt activity, MK-2206 2HC1 is a highly selective inhibitor of Akt1/2/3, iltefosine inhibits PI3K/Akt activity, and SK690693 is a pan-Akt inhibitor targeting Akt1/2/3. These and others are available from Selleck/Pfeizer.

4.1. Administration and Pharmaceutical Formulations

The therapeutic agents that reduce expression or biological activity of FOXM1 and CENPF, as described above, can be administered in a single formulation or in separate formulations. They can be administered either locally, for example by injection into the prostate or prostate tumor, or systemically such as by oral or intramuscular or intravascular injection. Where the therapeutic agent is an inhibitory oligonucleotide, the preferred route is oral administration. In embodiments of the invention, inhibitory oligonucleotides, nonoligonucleotides and small molecular therapeutic/active agents that reduce FOXM1 and CENPF expression or biological activity are combined for treating aggressive prostate cancer, or to slow or prevent progression of non-aggressive prostate cancer to an aggressive form. Active agents can be combined in a single pharmaceutical formulation or administered in separate formulations, on the same day or on different days. Multiple administration is typically required over the course of days, weeks, months or years.

Small molecule inhibitors of FOXM1 and CENPF expression or biological activity for use in embodiments of the invention may be present in the pharmaceutical compositions in the form of salts of pharmaceutically acceptable acids or in the form of bases. The therapeutic agents may be present in amorphous form or in crystalline forms, including hydrates and solvates. Preferably, the pharmaceutical compositions comprise a therapeutically effective amount.

Pharmaceutically acceptable salts of the therapeutic agents described herein include those salts derived from pharmaceutically acceptable inorganic and organic acids and bases. Examples of suitable acid salts include acetate, adipate, alginate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate, citrate, camphorate, camphorsulfonate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptanoate, glycerophosphate, glycolate, hemisulfate, heptanoate, hexanoate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethanesulfonate, lactate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oxalate, palmoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, salicylate, succinate, sulfate, tartrate, thiocyanate, tosylate and undecanoate salts. Other acids, such as oxalic, while not in themselves pharmaceutically acceptable, may be employed in the preparation of salts useful as intermediates in obtaining pharmaceutically acceptable acid addition salts.

Salts derived from appropriate bases include alkali metal (e.g., sodium and potassium), alkaline earth metal (e.g., magnesium), ammonium and N⁺(C₁₋₄ alkyl)₄ salts. It is anticipated that some embodiment include the quaternization of any basic nitrogen-containing groups of the therapeutic agents disclosed herein. Water or oil-soluble or dispersible products may be obtained by such quaternization.

The therapeutic agents of some embodiments are also meant to include all stereochemical forms of the therapeutic agents (i.e., the R and S configurations for each asymmetric center). Therefore, single enantiomers, racemic mixtures, and diastereomers of the therapeutic agents are within the scope of the invention. Also within the scope of the invention are steric isomers and positional isomers of the therapeutic agents. The therapeutic agents of some embodiments are also meant to include compounds which differ only in the presence of one or more isotopically enriched atoms. For example, therapeutic agents in which one or more hydrogens are replaced by deuterium or tritium, or the replacement of one or more carbons by ¹³C- or ¹⁴C-enriched carbon are within the scope of this invention.

The active agents and pharmaceutical compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration. Administration can also be pulmonary. Oligonucleotides with at least one 2′-O-methoxyethyl modification are believed to be particularly useful for oral administration.

In a preferred embodiment, the therapeutic agents of some embodiments are administered in a pharmaceutical composition that includes a pharmaceutically acceptable carrier, adjuvant, or vehicle. The term “pharmaceutically acceptable carrier, adjuvant, or vehicle” refers to a non-toxic carrier, adjuvant, or vehicle that does not destroy or significantly diminish the pharmacological activity of the therapeutic agent with which it is formulated.

Pharmaceutically acceptable carriers, adjuvants or vehicles that may be used in the compositions of some embodiments encompass any of the standard pharmaceutically accepted liquid carriers, such as a phosphate-buffered saline solution, water, as well as emulsions such as an oil/water emulsion or a triglyceride emulsion. Solid carriers may include excipients such as starch, milk, sugar, certain types of clay, stearic acid, talc, gums, glycols, or other known excipients. Carriers may also include flavor and color additives or other ingredients. The formulations of the combination of some embodiments may be prepared by methods well-known in the pharmaceutical arts and described herein. Exemplary acceptable pharmaceutical carriers have been discussed above. An additional carrier, Cremophor™, may be useful, as it is a common vehicle for Taxol.

The pharmaceutical compositions of some embodiments are prepared for oral administration, preferably as solid compositions. However, the pharmaceutical compositions may be administered by intravenous injection or by injection or infusion into the prostate gland or prostate tumor, parenterally, or via an implanted reservoir. Sterile injectable forms of the pharmaceutical compositions may be aqueous or oleaginous suspensions. These suspensions may be formulated according to techniques known in the art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution or suspension in a non-toxic parenterally acceptable diluent or solvent, for example as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium.

The pharmaceutical compositions employed in some embodiments may be orally administered in any orally acceptable dosage form, including, but not limited to, solid forms such as capsules and tablets. In the case of tablets for oral use, carriers commonly used include microcrystalline cellulose, lactose and corn starch. Lubricating agents, such as magnesium stearate, are also typically added. When aqueous suspensions are required for oral use, the active ingredient may be combined with emulsifying and suspending agents. If desired, certain sweetening, flavoring or coloring agents may also be added.

Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can comprise the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. Pharmaceutical compositions suitable for injection comprise sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. For intravenous administration, suitable carriers comprise physiological saline, bacteriostatic water, Cremophor EL™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the selected particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In some cases, isotonic agents are included in the composition, for example, sugars, polyalcohols such as manitol, sorbitol, or sodium chloride. Prolonged absorption of an injectable composition can be achieved by including in the composition an agent that delays absorption, for example, aluminum monostearate or gelatin.

Sterile injectable solutions can be prepared by incorporating the active compound in the specified amount in an appropriate solvent with one or a combination of ingredients enumerated above, as needed, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and other ingredients selected from those enumerated above or others known in the art. In the case of sterile powders for the preparation of sterile injectable solutions, the methods of preparation comprise vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

Oral compositions generally comprise an inert diluent or an edible carrier. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules, e.g., gelatin capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash. Pharmaceutically compatible binding agents, and/or adjuvant materials can be comprised as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.

4.2 Inhibitory Oligonucleotides for Clinical Use to Treat Aggressive Prostate Cancer

In the context of this invention, the term “oligonucleotide” refers to an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or mimetics thereof. This term includes oligonucleotides composed of naturally-occurring nucleobases, sugars and covalent internucleoside (backbone) linkages as well as oligonucleotides having non-naturally-occurring portions which function similarly. Such modified or substituted oligonucleotides are often preferred over native forms because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for nucleic acid target and increased stability in the presence of nucleases. As used herein an inhibitory oligonucleotide includes without limitation antisense, siRNA, shRNA, ribozymes and MIRs that reduce the expression of a targeted FOXM1 or CENPF gene or protein.

In certain aspects, the invention relates to a pharmaceutical composition comprising one or more inhibitory nucleic acids (inhibitory oligonucleotides) capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid, and a pharmaceutically acceptable carrier. In another aspect, the methods described herein relate to treating a subject with prostate cancer, especially aggressive prostate cancer, by administering (or otherwise contacting a prostate cancer cell with) a therapeutically effective amount of an inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid in a cancerous prostate cell, e.g., a cell of a subject. In the method the inhibitory nucleic acid is substantially complementary to the nucleotide sequence of the target (e.g. a nucleic acid encoding a FOXM1 or CENPF polypeptide). Such methods can be performed on a human or a non-human mammal by administering to a one of the inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid or pharmaceutical compositions described herein.

The invention also relates to a method for treating a subject who has been diagnosed with any other cancer or a disorder characterized by overexpression of FOXM1 and CENPF and wherein the subject can be treated by administration of inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid, thereby alleviating the symptoms associated with the overexpression of FOXM1 and CENPF.

A therapeutically effective amount a compound that reduces the expression or activity of FOXM1 and/or CENPF for the practice of the present invention can be further refined by one of ordinary skill in the art using known criteria including the age, weight and response of the individual patient, and interpreted within the context of the disease which is being treated or which is being prevented. In one embodiment, an effective amount is an amount of a compound that reduces the expression or activity of FOXM1 and/or CENPF, a pharmaceutical composition, or a medicine or medicament thereof that elicits the biological or medicinal response (such as inhibiting, preventing or treating) of a cancer in a tissue system, animal or human, that is being sought by a researcher, veterinarian, medical doctor, or other clinician.

In certain embodiments, the therapeutically effective amount of a compound that reduces the expression or activity of FOXM1 and/or CENPF can be delivered as a pharmaceutical composition. In certain embodiments, the pharmaceutical composition can be a product containing a compound that reduces the expression or activity of FOXM1 and/or CENPF, wherein the product comprises the specified ingredients in specified amounts, as well as any product that results, directly or indirectly, from such combinations of the specified ingredients in the specified amounts.

In other embodiments, the compositions described herein can be administered in a pharmaceutically acceptable form. In another embodiment, a pharmaceutically acceptable form can be a composition that is of sufficient purity or quality to be of use in the formulation of a pharmaceutical composition, medicine or medicament of the present invention. Since both human use and veterinary use are equally included within the scope of the present invention, a pharmaceutically acceptable formulation can include a pharmaceutical composition, medicine or medicament for either human or veterinary use.

In certain embodiments, the inhibitory nucleic acid that reduces the expression or activity of FOXM1 or CENPF (herein “a described inhibitory oligonucleotide”) can comprise is an inhibitory nucleic acid which hybridizes to at least a portion of a FOXM1 or CENPF nucleic acid to modify expression of a protein encoded by the nucleic acid. The oligonucleotide may match the target region exactly or may contain several mismatches. A variety of nucleic acid species are capable of modifying gene expression or modifying the activity of a polypeptide encoded therefrom. These include antisense RNA, shRNA, siRNA, microRNA, RNA and DNA aptamers, and decoy RNAs. Each of these nucleic acid species can be used in connection with the methods described herein to reduce the expression or activity of FOXM1 or CENPF.

In certain embodiments, the described inhibitory nucleic acid can be an siRNA comprising a double stranded structure containing from about 15 to about 50 base pairs, for example from about 21 to about 25 base pairs, and having a nucleotide sequence identical or nearly identical to an expressed target gene or RNA within the cell. Antisense nucleotide sequences include, but are not limited to: morpholinos, 2′-O-methyl polynucleotides, DNA, RNA and the like. RNA polymerase III transcribed DNAs contain promoters, such as the U6 promoter. These DNAs can be transcribed to produce small hairpin RNAs in the cell that can function as siRNA or linear RNAs that can function as antisense RNA. The inhibitory nucleic acid that reduces the expression or activity of FOXM1 or CENPF can contain ribonucleotides, deoxyribonucleotides, synthetic nucleotides, or any suitable combination such that the target RNA and/or gene is inhibited. In addition, these forms of nucleic acid can be single, double, triple, or quadruple stranded.

The described inhibitory nucleic acid can be produced chemically or biologically, or can be expressed from a recombinant plasmid or viral vector.

A described inhibitory nucleic acid can additionally be a short hairpin RNA (shRNA).

The hairpin RNAs can be synthesized exogenously or can be formed by transcribing from RNA polymerase III promoters in vivo. Examples of making and using such hairpin RNAs for gene silencing in mammalian cells are described in, for example, Paddison et al., 2002; McCaffrey et al., 2002; McManus et al., 2002; Yu et al., 2002. Such hairpin RNAs are engineered in cells or in an animal to ensure continuous and stable suppression of a desired gene. It is known in the art that siRNAs can be produced by processing a hairpin RNA in the cell.

In certain embodiments, shRNAs suitable for use with the methods described herein can be a shRNA having, consisting essentially of, or comprising the sequence of any of SEQ ID NOs 1-4. In certain embodiments, an shRNA having, consisting essentially of, or comprising the sequence of SEQ ID NO: 1 or 2 can be useful for reducing the expression of FOXM1 in connection with the methods described herein. In certain embodiments, an shRNA having, consisting essentially of, or comprising the sequence of SEQ ID NO: 3 or 4 can be useful for reducing the expression of CENPF in connection with the methods described herein.

Described inhibitory nucleic acids can be designed and synthesized to include a region of noncomplementarity (e.g., a region that is 3, 4, 5, or 6 nucleotides long) flanked by regions of sufficient complementarity to form a duplex (e.g., regions that are 7, 8, 9, 10, or 11 nucleotides long) with a target RNA. Inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid can be 18-100 nucleotides in length and, in certain embodiments can be designed by one of skill in the art to undergo processing to become mature. For example, mature miRNAs can have a length of 19-30 nucleotides, 21-25 nucleotides, particularly 21, 22, 23, 24, or 25 nucleotides, whereas miRNA precursors typically have a length of about 70-100 nucleotides and have a hairpin conformation.

The described inhibitory nucleic acid can be an oligomers or a polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or both or modifications thereof. This term includes oligonucleotides composed of naturally occurring nucleobases, sugars, and covalent internucleoside (backbone) linkages as well as oligonucleotides having non-naturally occurring portions that function similarly.

A described inhibitory nucleic acid can include a nucleotide sequence sufficiently complementary to hybridize to an FOXM1 or CENPF target sequence. In certain embodiments, the sufficient complementarity can be of about 12 to 25 nucleotides, about 13 to 23 nucleotides, about 14 to 23 nucleotides or about 15 to 23 nucleotides. It is contemplated that a nucleic acid fragment of the present invention may be almost any length. A general size range for the Inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid themselves will be 20 to 90-100 bases. It will be readily understood that intermediate lengths, such as 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99, are contemplated as well.

In certain non-limiting embodiments, a described inhibitory nucleic acid is considered to be targeted FOXM1 or CENPF if (1) the stability of the target gene transcript (e.g. FOXM1 or CENPF) is reduced in the presence of the inhibitory nucleic acid as compared with its absence; and/or (2) the inhibitory nucleic acid shows at least about 90%, more preferably at least about 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% precise sequence complementarity with the target transcript (e.g. FOXM1 or CENPF) for a stretch of at least about 17, more preferably at least about 18 or 19 to about 21-23 nucleotides; and/or (3) the inhibitory nucleic acid hybridizes to the target transcript under stringent conditions.

The described inhibitory nucleic acid can also be produced biologically using an expression vector.

The described inhibitory nucleic acids can be synthesized in vivo by a cell-based system or in vitro by chemical synthesis. Inhibitory nucleic acids capable of reducing expression or activity of a protein encoded by FOXM1 or CENPF can be constructed using chemical synthesis and/or enzymatic ligation reactions using procedures known in the art.

A described inhibitory nucleic acid can include a region of sufficient complementarity to the target nucleic acid (e.g., target FOXM1 or CENPF), and is of sufficient length in terms of nucleotides, such that the miRNA inhibitory nucleic acid forms a duplex with the target nucleic acid. An inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid is, or includes, a region that is at least partially, and in some embodiments fully, complementary to the target RNA (e.g., target FOXM1 or CENPF). It is not necessary that there be perfect complementarity between the Inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid and the target, but the correspondence must be sufficient to enable the oligonucleotide agent, or a cleavage product thereof, to modulate (e.g., inhibit) target gene expression.

An inhibitory nucleic acid can be synthesized to include a modification that imparts a desired characteristic. For example, the modification can improve stability, hybridization thermodynamics with a target nucleic acid, targeting to a particular tissue or cell-type, or cell permeability, e.g., by an endocytosis-dependent or -independent mechanism. Modifications can also increase sequence specificity, and consequently decrease off-site targeting.

The described inhibitory nucleic acid can be further stabilized against nucleolytic degradation such as by the incorporation of a modification, e.g., a nucleotide modification. The inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid can include a phosphorothioate at least the first, second, or third internucleotide linkage at the 5′ or 3′ end of the nucleotide sequence. In certain embodiments, the inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid can include a 2′-modified nucleotide, e.g., a 2′-deoxy, 2′-deoxy-2′-fluoro, 2′-O-methyl, 2′-O-methoxyethyl (2′-O-MOE), 2′-O-aminopropyl (2′-O-AP), 2′-O-dimethylaminoethyl (2′-O-DMAOE), 2′-O-dimethylaminopropyl (2′-O-DMAP), 2′-O-dimethylaminoethyloxyethyl (2′-O-DMAEOE), or 2′-O—N-methylacetamido (2′-O-NMA). In a particular embodiment, the inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid includes at least one 2′-O-methyl-modified nucleotide, and in some embodiments, all of the nucleotides of the inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid include a 2′-O-methyl modification.

The described inhibitory nucleic acid can be further modified so as to be attached to a ligand that is selected to improve stability, distribution or cellular uptake of the agent, e.g., cholesterol. Such non-nucleotide moiety can be attached, e.g., to the 3′ or 5′ end of the oligonucleotide agent. In one embodiment, a cholesterol moiety is attached to the 3′ end of the inhibitory nucleic acid. In certain embodiments, the inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid includes a modification that improves targeting. Examples of modifications that target single-stranded oligonucleotide agents to particular cell types include carbohydrate sugars such as galactose, N-acetylgalactosamine, mannose; vitamins such as folates; other ligands such as RGDs and RGD mimics; and small molecules including naproxen, ibuprofen or other known protein-binding molecules.

In one embodiment, a described inhibitory nucleic acid, such as a single-stranded oligonucleotide agent, can have a nucleotide sequence that is substantially identical to a portion of a nucleic acid encoding FOXM1 or CENPF. Single-stranded oligonucleotide agents that are substantially identical to at least a portion of a nucleic acid encoding FOXM1 or CENPF, such as those described above, can be administered to a subject to treat a subject having, or at risk of having, a cancer.

A described inhibitory nucleic can be delivered into a cell in any of a variety of forms, including as naked plasmid or other DNA, formulated in liposomes, in an expression vector, which includes a viral vector (including RNA viruses and DNA viruses, including adenovirus, lentivirus, alphavirus, and adeno-associated virus). The amount of nucleic acid needed to sequester an Id protein in the cytoplasm can be readily determined by those of skill in the art, which also can vary with the delivery formulation and mode and whether the nucleic acid is DNA or RNA.

The described inhibitory nucleic acid can further be in isolated form or can be part of a pharmaceutical composition used for the methods described herein, particularly as a pharmaceutical composition formulated for parental administration. The pharmaceutical compositions can contain one or more inhibitory nucleic acid agents, and in some embodiments will contain two or more inhibitory nucleic acid agents, each one directed to a different target gene. For example, in certain embodiments, the pharmaceutical composition can comprise at least one inhibitory nucleic acid directed to FOXM1 and at least one inhibitory nucleic acid directed to CENPF.

In another aspect, the described inhibitory nucleic acids capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid can be expressed from transcription units inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. Viral vectors suitable for producing inhibitory nucleic acids capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. The recombinant vectors capable of expressing the inhibitory nucleic acids capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid can be delivered as described above, and can persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of nucleic acid molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the inhibitory nucleic acids capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid interacts with the target RNA and inhibits miRNA activity. A number of viruses can be used in connection with the methods described herein, including papovaviruses, e.g., SV40, adenovirus, vaccinia virus, adeno-associated virus, herpesviruses including HSV and EBV, and retroviruses of avian, murine, and human origin. In certain embodiments, lentiviral vectors can be used in connection with the methods described herein. In certain embodiments, the lentiviral vector can be a doxycycline-inducible lentiviral vector engineered to express one or more shRNAs against FOXM1, one or more an shRNAs against CENPF, or to express a plurality of shRNAs, wherein one or more is an shRNA against FOXM1 and one or more is an shRNA against CENPF.

Delivery of the inhibitory nucleic acid-expressing vectors can be systemic, such as by intravenous or intra-muscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell (for a review see Couture et al., Trends in Genetics 12:510, 1996).

4.3 Pharmaceutical Formulation and Clinical Use of Inhibitory Oligonucleotides

Because nucleases that cleave the phosphodiester linkage in DNA are expressed in almost every cell, unmodified DNA molecules such as inhibitory oligonucleotides are generally modified to resist degradation. Additionally, most targets of antisense are located inside cells, and getting nucleic acids across cell membranes is taken into account. For clinical use, inhibitory oligos that have modified nucleotides that resist degradation are preferred. Additionally, other molecules may be conjugated to antisense molecules in order to improve their ability to target certain cells or to cross barriers like cell membranes or the blood brain barrier.

Chemical modifications of inhibitory oligonucleotides like antisense can significantly affect their bioavailability. Phosphorothioate modification of the antisense molecule promotes adhesion to cell surface proteins. Conjugation of a positively charged arginine-rich peptide to PMO-modified antisense oligonucleotides could be used to improve cellular delivery.

Intracellular delivery systems with potential in vivo applications include antisense oligonucleotide conjugation with cationic lipid carriers, carrier molecules that bind with cell-specific receptors, cyclodextrins, dendrimers, microparticles, and macromolecules. These delivery systems can enhance intracellular delivery either by protecting antisense oligonucleotide from nuclease degradation and/or by promoting absorptive endocytosis.

Included in the macromolecule class are cell-penetrating peptides (CPPs), short peptide sequences with a net positive charge that are conjugated to the antisense oligonucleotide via a disulphide bridge. Commonly used CPPs include penetratin, HIV TAT peptide 48-60, and transportan. Further, the addition of dioleylphosphatidylethanolamine to liposome delivery systems results in the destabilization of endosomal membranes and promotion of release of the antisense oligonucleotide after endocytosis.

The enhancement of bioavailability after oral administration can be enhanced by encapsulating in an inert, biodegradable albumin polymer matrix which has been shown to increase bioavailability from 9%, up to 70%. Moreover, the other pharmacokinetic parameters including half-life (t_(1/2)) and volume of distribution (V_(d)) increased for the microencapsulated form compared to the solution form of the drug (Uddin et al., 2013),

A few nanoparticle-based siRNA delivery systems have been approved by the FDA and are in clinical trials for cancer therapy. All the nanoparticle-formulated siRNA delivery systems for cancer therapy that are currently in clinical trials are based on polymers or liposomes.

Nanoparticles conjugated to the targeting ligand for effective siRNA delivery increase the chance of binding the tumor surface receptor; however, the process also increases the overall size of the nanoparticle. The PEG coating of nanoparticles reduces uptake by RES, resulting in enhanced circulatory half-life, but reduces targeting specificity because PEG molecules sterically disrupt selective conjugation. Thus, the selection of appropriate cell-specific targeting moieties and careful design of stable and potent nanoparticle delivery systems is required for future development. Various nanoparticle-based delivery systems such as cationic lipids, polymers, dendrimers, and inorganic nanoparticles have been demonstrated to provide effective and efficient siRNA delivery in vitro and in vivo.

Antisense oligonucleotides can be delivered directly by systemic administration such as using oral formulations or stereotactic injection into prostate or prostate tumor, typically in saline with chemical modifications to enable uptake. Their phosphorothioate backbone binds to serum proteins, slowing excretion by the kidney. The aromatic nucleobases also interact with other hydrophobic molecules in serum and on cell surfaces. Many types of cells in vivo express surface receptors that actively take up oligonucleotides; these are often lost when cells are cultured, which explains why lipid seems more important for delivering ASOs in culture than in vivo.

Delivery is more challenging for duplex RNAs than single-stranded oligonucleotides. In an siRNA, all of the aromatic nucleobases are on the inside, leaving only heavily hydrated phosphates on the outside of the duplex. This hydrated surface interacts poorly with cell surfaces and is rapidly excreted in the urine. Thus researchers have invested heavily in the development of delivery vehicles for siRNAs. The predominant technologies for delivering siRNAs involve complexing the RNA with cationic and neutral lipids, although encouraging results have also been obtained using peptide transduction domains and cationic polymers. Including PEGylated lipids in the formulation prolongs the circulating half-life of the particles. Conjugation of cholesterol to one strand of the siRNA gave effective knockdown in the liver of mice, but the quantities of material required (50 mg/kg) were several orders of magnitude higher than current lipid-based formulations (as low as 0.01 mg/kg).

One type of optimization of single-stranded DNA or RNA oligonucleotides is the use of chemical modifications to increase the nuclease resistance such as the introduction of phosphorothioate (PS) linkages in place of the phosphodiester bond. This modification greatly improved stability towards digestion by nucleases. PS linkages also improved binding to serum proteins in vivo, increasing half-life and permitting greater delivery of active compound to tissues. ASOs that only contain PS modifications were capable of producing antisense effects inside cells, but potencies were not always high nor were reliable results routine.

Chemical modifications can also improve potency and selectivity by increasing binding affinity of oligonucleotides for their complementary sequences. Widely used modifications include 2′-O-methyl (2′-O-Me), 2′-fluoro (2′-F), and 2′-O-methoxyethyl (2′-MOE) RNA. Even more affinity can be gained using oligonucleotides modified with locked nucleic acid (LNA), which contains a methylene bridge between the 2′ and 4′ position of the ribose. This bridge “locks” the ribose ring in a conformation that is ideal for binding, leading to high affinity for complementary sequences. Related bridged nucleic acid (BNA) compounds have been developed and share these favorable properties. Their high affinity has permitted the development of far shorter oligonucleotides than previously thought possible which nonetheless retain high potency. The chemistry for introducing 2′-O-Me, 2′-MOE, 2′-F, or LNA into oligonucleotides is compatible with DNA or RNA synthesis, allowing chimeras with DNA or RNA bases to be easily obtained. This compatibility allows the properties of chemically modified oligonucleotides to be fine-tuned for specific applications—a major advantage for development that makes LNAs and other BNAs convenient tools for many applications.

Over the past decade, double-stranded short interfering RNAs (siRNAs) have become widely used tools for silencing gene expression. When a duplex RNA enters cells it binds the protein machinery of the RNA induced silencing complex (RISC). Synthetic RNAs used for gene silencing are usually 19-22 bp duplexes. This length is sufficient to form a stable duplex and be recognized by RISC, but short enough to avoid most of the strong interferon response provoked by duplexes greater than 30 bp in length.

Since publication of the first report of gene silencing in mammalian cells in 2001, siRNAs have been the subject of thousands of experimental studies aimed at examining function. While antisense oligonucleotides continue to be used for gene silencing, the robust nature of siRNAs and the relative ease of identifying active siRNAs have made them a favored silencing tool for many laboratories.

Unmodified duplex RNA is surprisingly stable and chemical modification of siRNAs is usually not essential for silencing gene expression in cultured cells. In vivo, however, unmodified siRNAs are not highly active and chemical modification can significantly improve their properties. Chemically modified siRNAs can feature improved nuclease stability and an associated increase in duration of action. Unmodified RNA is also rapidly cleared and chemical modification, complexation with carrier agent, and local delivery to a disease target can help achieve improved in vivo results.

In vivo, the choice of ASO versus siRNA is unsettled and will continue to evolve over the next decade. For example, in animal models of Huntington's disease, antisense oligonucleotides or siRNAs have been infused directly into the central nervous system. In the case of single-stranded oligonucleotides, researchers observed wide distribution throughout the mouse CNS including deep-brain penetration. In contrast, others found that siRNA infused into the monkey brain penetrated into brain tissue only up to about 12 mm from the site of infusion.

ASOs and siRNAs share important similarities as drug candidates. Both platforms are intended to modulate gene expression. Both are nucleic acids and contain an antisense strand intended to recognize a target mRNA. They also have important differences. ASOs have one strand while siRNAs have two, a basic fact that may lower cost and simplify delivery. On the other hand, siRNAs have proven to be a more robust technology in cell culture in the hands of most users. It is not clear whether this will be true in vivo, but the possibility that siRNAs might have superior potency for at least some applications is a major driving force for their continued development.

An example of the new wave of promising antisense oligonucleotides is Mipomersen, an ASO from ISIS Pharmaceuticals designed to inhibit expression of Apo-B. Mipomersen is a gapmer containing phosphorothioate-modified DNA and 2′-O-MOE-RNA. Data from animal models show a robust and prolonged repression of target apo-B expression. In patients, the desired physiologic response upon systemic administration was demonstrated in four separate Phase III clinical trials. Some toxic effects have been noted, and while these have been relatively mild they may (at least initially) limit the patient population to patients who are at the most severe risk for atherosclerosis.

As of 2013, eleven other traditional antisense oligonucleotides were in advanced clinical trials. Targets relevant to cancer are the most highly represented, but there are also ASOs in trials against asthma, corneal neovascularization and ulcerative colitis. Many of these ASOs contain optimized chemistry and are taking advantage of the lessons learned over the past two decades in terms of delivery.

Three splice-switching ASOs are in Phase II or III clinical trials, all of them for treatment of Duchenne muscular dystrophy. Prosenza has developed 2′-OMe phosphorothioate oligonucleotides while AVI BioPharma has favored development of morpholino oligomers. Both drugs show promise in clinical development.

A decade after the first siRNA experiments, at least dozen siRNA drugs are in clinical development. The four most advanced are in Phase II trials. As with ASOs, some of the earliest drugs to enter trials were very simple “first generation” siRNAs containing no chemical modifications.

The oligonucleotides used in accordance with various embodiments may be conveniently and routinely made through the well-known technique of solid phase synthesis. Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, Calif.). Any other means for such synthesis known in the art may additionally or alternatively be employed.

Therapeutic administration of inhibitory nucleic acids capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid to cells for use with the methods described herein include any method by which a nucleic acid (e.g., DNA), as known to one of ordinary skill in the art. For treatment of aggressive prostate cancer, delivery is preferably by oral administration or injection into the prostate gland or tumor or both. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by ionophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors.

In certain embodiments, the inhibitory nucleic acids capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid can be delivered to an organelle, a cell, a tissue, a tumor or an organism via one or more injections (i.e., a needle injection), such as, for example, subcutaneously, intradermally, intramuscularly, intravenously, intraperitoneally, etc.

A described inhibitory nucleic acid or other active agent can be incorporated into pharmaceutical compositions suitable for administration. For example, pharmaceutical compositions can comprise one or more the inhibitory nucleic acids capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid and a pharmaceutically acceptable carrier. As used herein the language “pharmaceutically acceptable carrier” is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.

A described inhibitory nucleic acid may be provided in sustained release compositions. The use of immediate or sustained release compositions depends on the nature of the condition being treated. If the condition consists of an acute or over-acute disorder, treatment with an immediate release form can be conducted over a prolonged release composition. Alternatively, for certain preventative or long-term treatments, a sustained release composition may be appropriate.

A described inhibitory nucleic acid can be administered in a single dose or in multiple doses. Where the administration of the active agent is by infusion, the infusion can be a single sustained dose or can be delivered by multiple infusions. Injection of the agent can be directly into the tissue at or near the site of aberrant or unwanted target gene expression. Multiple injections of an inhibitory nucleic acid capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid can be made into the tissue-for example, into the prostate gland, into the prostate tumor, or near the tumor.

In addition to treating pre-existing aggressive or non-aggressive prostate cancers, active agents capable of reducing expression or activity of a protein encoded by a FOXM1 or CENPF nucleic acid can be administered prophylactically in order to prevent or slow the conversion of a non-aggressive prostate cancer to an aggressive form. The described inhibitory nucleic acids can be employed in combination therapies, meaning that the present compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutic agents or medical procedures. The combination of therapies (therapeutic agents or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutic agents and/or procedures and the desired therapeutic effect to be achieved. It will also be appreciated that the therapies employed can achieve a desired effect for the same disorder (for example, a compound described herein can be administered concurrently with another therapeutic agent used to treat the same disorder), or they can achieve different effects (e.g., control of any adverse effects).

Known agents useful for treating cancers can be combined with the described inhibitory nucleic acids to treat a cancer wherein both FOXM1 and CENPF are elevated, such as a prostate cancer. For example, a described inhibitory nucleic acid can be administered with another therapeutic agent simultaneously or sequentially in separate unit dosage forms or together in a single unit dosage form.

The described inhibitory nucleic acids and methods of the present invention are useful for individuals who have received prior medication for a cancer, as well as individuals who have received no prior medication for a cancer. Individuals of any age can be treated by the methods compositions of the invention.

It is understood that the appropriate dose of an active agent depends upon a number of factors within the knowledge of the ordinarily skilled physician, veterinarian, or researcher. The dose(s) vary, for example, depending upon the identity, size, and condition of the subject or sample being treated, further depending upon the route by which the active agents and pharmaceutical compositions are to be administered, and the effect which the practitioner desires the an active agent to have. It is furthermore understood that appropriate doses of an active agent depend upon the potency with respect to the expression or activity to be modulated. Such appropriate doses may be determined using the assays described herein. When one or more of these active agents are to be administered to an animal (e.g., a human) in order to reduce expression or activity of FOXM1 and CENPF protein, a relatively low dose may be prescribed at first, with the dose subsequently increased until an appropriate response is obtained. In addition, it is understood that the specific dose level for any particular subject will depend upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, gender, and diet of the subject, the time of administration, the route of administration, the rate of excretion, any drug combination, and the degree of expression or activity to be modulated.

5. Examples 5.1 Example 1 Experimental Procedures

Pilate perturbagen studies were performed to evaluate optimal dosage and scheduling. As an example, rapamycin treatment of NP mice involved treating mice for 1, 2, or 5 days and concentrations varied from 10, 25 and 50 mg/kg. Following treatment, expression profiling was done on prostate tumors to evaluate the dose and schedule that produced the optimal range of gene expression changes. The number of differentially expressed genes at different p-value thresholds (0.01 or 0.05) with or without a 1.5-fold change (FC) cut-off was determined. The perturbagen studies were used for assembly of the mouse prostate cancer interactome.

The primary gene expression profile dataset used for ARACNe-based reverse engineering was Taylor et al (GSE21034), which consists of primary human prostatectomy samples, adjacent normal tissue, and metastases arrayed on a Affymetrix human Exon 1.0 ST microarray platform (Taylor et al., 2010). Additional expression profile datasets used were: (i) Yu et al (GSE6919): primary human prostatectomy samples and adjacent normal tissue arrayed on a Affymetrix U95a, U95b and U95c microarray platforms (ii) Wang et al (a) (GSE17951): primary human prostatectomy samples, prostate biopsies, and normal prostate arrayed on a Affymetrix U133Plus2.0 platform; (iii) Wang et al (b) (GSE8218): primary human prostatectomy samples and normal prostate on a Affymetrix U133A platform; and (iv) Balk (GSE32269): biopsies of primary tumors from subjects with hormone-naïve prostate cancer and of bone marrow with confirmed tumor content from subjects with metastatic castration resistant prostate cancer (CRPC) on Affymetrix U133A platform. Available clinico-pathological information is provided in the table of FIG. 5.

For expression profiling analyses, prostate tumors were macrodissected, and the content of tumor/cellular atypia was verified by H&E analyses. Total RNA was isolated from prostate tissues/tumors using a MagMAX-96 total RNA isolation kit and biotin-labeled using the Illumina TotalPrep RNA Amplification Kit (Life Technologies). The resulting cRNA was hybridized on mouseWG-6 v2 BeadArrays (Illumina). Slides were scanned using an iScan (Illumina) and the resulting files were uploaded and background-corrected in BeadStudio 3.1.3.0 (Illumina, Inc.). Expression profiling data were normalized using standard variance stabilizing transformation (VST) and robust spline normalization (RSN) with lumiT and lumiN functions from lumi library, in R-system v2.14.0 (The R Foundation for Statistical Computing, ISBN 3-900051-07-0). The raw and normalized data files are deposited in Gene Expression Omnibus (GEO), accession number GSE53202.

Immunostaining was performed as described in Irshad et al., 2013. Immunostaining for FOXM1 or CENPF was performed on adjacent sections of each TMA slide. For immunofluorescent staining on cells in culture, 1×10⁵ cells infected with the experimental or control shRNA were seeded in triplicate and grown in culture slides (BD Biosciences) for three days in the presence of 0.5 pg/ml of doxycycline. Cells were washed with PBS, fixed in ice cold acetone and permeabilized in 0.25% Triton X-100 in PBS and stained with antibodies for FOXM1 and CENPF (see Table 2, below). Images of the cellular localization of FOXM1 and CENPF were obtained using a Leica TCS SP5 spectral confocal microscope. Protein levels were determined by percent of staining (i.e. from 0 to 100%) and intensity level of staining (i.e., 0, 1, 2, or 3) in each tumor sample. We defined a composite protein level by multiplying percent of staining and its intensity level for each tumor sample, for FOXM1 or CENPF. Composite protein level exceeding 100 were considered elevated.

Statistical analysis was performed with survcomp package using R v2.14.0. Cox proportional hazard model was estimated with the surv and coxph functions. Kaplan-Meier survival analysis was performed using surv, survfit, and survdiff functions. Concordance indexes (c-index) were estimated and compared using coxp and concordance.index (counting ties) and cindex.comp functions.

Predicting additive effects by extrapolating individual effects of silencing FOXM1 or CENPF was evaluated as follows. To quantitatively evaluate synergy versus additivity of the tumor growth rate, an estimate of an “additive” effect was projected using a log-linear regression model, which assumes that the silencing of either master regulator individually induces a fractional reduction in tumor growth from that of control mice. The difference between the projected “additive” model versus the actual observed consequence of co-silencing was calculated using a one-sample t-test.

MARINa was used to estimate the activity levels of FOXM1 and CENPF, based on their ARACNe-inferred transcriptional targets, for each sample (i.e., each subject) in the Sboner and Glinsky human prostate cancer datasets (FIG. 5) (Glinsky et al., 2004; Sboner et al., 2010). The activity was defined as elevated if activated targets were positively enriched in the sample signature (i.e., positive NES) and at the same time repressed targets were negatively enriched in the sample signature (i.e., negative NES) and these enrichment scores fell into the upper/lower 35% percentile of NES distribution. Subjects were then divided into four groups: (i) those with non-elevated inferred activity for FOXM1 and CENPF; (ii) those with elevated inferred activity only for FOXM1; (iii) those with elevated inferred activity only for CENPF; and (iv) those with elevated inferred activity for both FOXM1 and CENPF. For these and all subsequent analyses, association with disease outcome was evaluated using Kaplan-Meier survival analysis calculated along with the log-rank p value using Surv, survfit, and survdiff functions from survcomp package in R v 2.14.0.)

Gene silencing of FOXM1 and CENPF as well as forced expression of FOXM1 were done using lentiviral shRNAs or expression vectors (Open Biosystems and CCSB Human ORFeome Library, respectively). Functional studies were done in four independent human cancer cell lines, which were obtained from ATCC. All experiments using animals were performed according to protocols approved by the Institutional Animal Care and Use Committee (IACUC) at Columbia University Medical Center.

Silencing was performed using the pTRIPZ lentiviral vector (Open Biosystems), which express an shRNAmir (microRNA-adapted shRNA, hereafter referred to as shRNA) and, for functional analysis, a tRFP fluorescent reporter under the control of a tetracycline responsive element (TRE) promoter such that expression of the shRNA can be induced by addition of doxycycline (0.5 pg/ml). For two-color fluorescence analyses, which were used for selection of cells expressing two different shRNA, the pTRIPZ vector was engineered to express eGFP using the AgeI and ClaI sites to replace the tRFP cassette. Following induction with doxycycline, cells infected with the pTRIPZ-RFP virus are detected by RFP expression (red), those infected with the pTRIPZ-GFP virus by GFP expression (green), and those infected with both pTRIPZ-RFP/pTRIPZ-GFP virus by expression of both tRFP and the eGFP (yellow). The shRNAs used to silence FOXM1 and CENPF were purchased from Open Biosystems; sequences are provided in Table 1. Unless otherwise indicated, analyses were done using two alternative shRNA and co-silencing was done using each combination of the experimental or control shRNA lentivirus.

TABLE 1 Sequences of shRNA and Primers for this study Sequence SEQ Purpose and name ID shRNA Clone ID NO Mature antisense FOXM1 shRNA#1 V3THS_283849 1 ATAATTAGAGGATAATTTG FOXM1 shRNA#2 V3THS_396941 2 TGATGGTCATGTTCCGGCG CENPFshRNA#1 V2THS_115502 3 ATCTGATTCACTCAGTCTG CENPF shRNA#2 V2THS_115504 4 TTTCTTCCAACAGTAACTG Scramble shRNA RH54743 N/A SEQ SEQ Real Time ID ID qPCR NO Forward NO Reverse FOXM1  5 CGTCGGCCACTGATTCTCAAA 19 GGCAGGGGATCTCTTAGGTTC CENPF  6 CTCTCCCGTCAACAGCGTTC 20 GTTGTGCATATTCTTGGCTTGC BRCA1  7 GCTCGTGGAAGATTTCGGTGT 21 TCATCAATCACGGACGTATCATC BUB1  8 AAATGACCCTCTGGATGTTTGG 22 GCATAAACGCCCTAATTTAAGCC KI67  9 GGGCCAATCCTGTCGCTTAAT 23 GTTATGCGCTTGCGAACCT CYCLIN A2 10 CGCTGGCGGTACTGAAGTC 24 GAGGAACGGTGACATGCTCAT TIMELESS 11 TCTGATCCGCTATTTGAGGCA 25 GGCAGAAGGTCGCTCTGTAG CDC25 12 ACGCACCTATCCCTGTCTC 26 CTGGAAGCGTCTGATGGCAA TRIP13 13 ACTGTTGCACTTCACATTTTCC 27 TCGAGGAGATGGGATTTGACT PLK1 14 AAAGAGATCCCGGAGGTCCTA 28 GGCTGCGGTGAATGGATATTTC HMMR 15 ATGATGGCTAAGCAAGAAGGC 29 TTTCCCTTGAGACTCTTCGAGA MYBL2 16 CCGGAGCAGAGGGATAGCA 30 CAGTGCGGTTAGGGAAGTGG ACTIN 17 GTCTGCCTTGGTAGTGGATAATG 31 TCGAGGACGCCCTATCATGG GAPDH 18 TGTGGGCATCAATGGATTTGG 32 ACACCATGTATTCCGGGTCAAT ChiP FOXM 33 CCGGAGCTTTCAGTTTGTTC 41 CGGAATGCCGAGACAAGG CENPF 34 CACCTCCAGTAGAGGGGCTTG 42 TACCTCCACGCCTATTGGTC AURKA 35 AGGACAAGGGCCTTCTTAGG 43 TAGTGGGTGGGGAGACAGAC AURKB 36 GGGGTCCAAGGCACTGCTAC 44 GGGGCGGGAGATTTGAAAAG BIRC5 37 CCATTAACCGCCAGATTTGA 45 TGTAGAGATGCGGTGGTCCT CDC25 38 AAGAGCCCATCAGTTCCGCTTG 46 CCCATTTTACAGACCTGGACGC PLK1 39 CCAGAGGGAGAAGATGTCCA 47 GTCGTTGTCCTCGAAAAAGC CYCLIN B2 40 TCCTTTGCCGAAAGCTAGAG 48 GCAACTGCCAATCTGAAAAAG

Lentiviral particles were made using the 2nd generation packaging vectors, psPAX2 and pMD2.G (Addgene) in HEK-293T cells (ATCC), and concentrated using the Lenti-X Concentrator reagent (Clonetech). Human prostate cancer cells used in this study were DU145, PC3, LNCaP, and 22Rv1 (ATCC). Following infection with the lentiviruses, cells were selected using 4 μg/ml of puromycin for three days, following which shRNA expression was induced by addition of 0.5 μg/ml of doxycycline. The optimal time-point for silencing was determined to be 72h following induction and used for all analyses, unless otherwise indicated. For enrichment of shRNA-expression, single-cell suspensions of the induced cells were FACS sorted on a BD-FACSAria cell sorter (BD biosciences) using the FITC (emission wavelength 525 nm, GFP positive) and/or PE-A (627-702 nm emission wavelength, RFP positive) channels and cells having the 20% highest-level expression were collected and used for analyses. Silencing of FOXM1 and CENPF RNA and protein were confirmed by qPCR and western blot analyses, respectively. Sequences of primers used for real time PCR are provided above in Table 1; antibodies are described in Table 2, with antibodies for immunohistochemistry indicated by the initials IHC.

TABLE 2 Antibodies used in this study Description Source Type Dilution Use FOXM1 Abcam, Mouse 1:1000 Western blot, (human) Ab550066 monoclonal IF FOXM1 Abcam, Mouse 1:400 IHC (human) Ab550066 monoclonal CENPF Abcam, Rabbit 1:200 Western blot, (human) Ab5 polyclonal IF CENPF Abcam, Mouse 1:400 IHC (human) Ab90 monoclonal pAKT Cell Signaling Rabbit 1:1000 Western blot #9271 polyclonal pERK Cell Signaling Rabbit 1:500 Western blot #9101 polyclonal pS6 Cell Signaling Rabbit 1:1000 Western blot #2211 polyclonal Actin Cell Signaling Rabbit 1:2000 Western blot 4970 polyclonal PARP Cell Signaling Rabbit 1:1000 Western blot #9542 polyclonal V5 Invitrogen Mouse 1:5000 Western blot, #R96025 monoclonal ChIP V5 Sigma Mouse 0.2 μg IP #A7345 monoclonal

Determining mRNA expression of FOXM1 or CENPF or both, total RNA was isolated from lentiviral-infected cells using TRIZOL and hybridized on Illumina Human HT-12 v4 Expression BeadChip Arrays. Hybridization and expression data processing were done as described above. Differential gene expression analysis was estimated with student t-test using p<0.05 as significant.

5.2 Example 2 Method of Discovery Gene Profiling

The t-Distributed Stochastic Neighbor Embedding (t-SNE) is a machine learning algorithm for dimensionality reduction. It is a nonlinear dimensionality reduction technique that is particularly well suited for embedding high-dimensional data into a space of two or three dimensions, which can then be visualized in a scatter plot. Specifically, it models each high-dimensional object by a two- or three-dimensional point in such a way that similar objects are modeled by nearby points and dissimilar objects are modeled by distant points. In the illustrated embodiment, the gene expression data is reduced to the two dimensions V1 and V2. The gene expression data was divided into 6 classes associated with normal cells adjacent to a tumor (AdjN), four Gleason scores (G6, G7, G8, and G9 or more), and metastasized (met). This analysis was done to evaluate the relative heterogeneity of human and mouse datasets used to assemble the prostate cancer interactomes. FIG. 1A depicts t-SNE analysis of the Taylor dataset relative to Gleason score. Each point is the two dimensional representation of the relative expression of many genes. The 26,445 genes are considered in the t-SNE analysis. Each point is the two dimensional representation of the similarity and divergence between the data sample (i.e., gene expression profile) and all other data samples.

Interactomes

Regulatory networks (interactomes) for human and mouse prostate cancer were generated using the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) (Basso et al., 2005; Margolin et al., 2006b). ARACNe is an unbiased algorithm that infers transcriptional interactions by computing the mutual information between each transcriptional regulator (transcription factors and co-factors) and its potential targets, and then by removing indirect interactions using the Data Processing Inequality (DPI). For optimal analysis, ARACNe requires large datasets of gene expression profiles (≧100) having significant endogenous (i.e., genetic) and/or exogenous (i.e., perturbation-induced) heterogeneity. Thus ARACNe analysis was performed on the Taylor data set.

ARACNe was run independently on the human and mouse datasets using a conservative mutual information threshold (p≦1.0×10⁻⁹, e.g., p≦0.05, Bonferroni corrected for all candidate interactions). This resulted in highly robust regulatory networks in which the human interactome represented 249,896 interactions between 2,681 transcriptional regulators and their inferred target genes, while the mouse interactome represented 222,787 interactions for 2,072 transcriptional regulators.

FIG. 2A is a block diagram and graph that illustrates example interactomes for human and mouse models with prostate cancer, according to an embodiment. ARACNE sub-networks from the human and the mouse prostate cancer interactomes highlight selected conserved transcriptional regulators. The scaled size of the transcriptional regulator nodes (filled circles) indicates the level of conservation while the relative distance between them approximates the strength of their association.

The suitability of these mouse and human interactomes for cross-species interrogation was next evaluated by developing a novel computational approach to assess the global conservation of their transcriptional programs.

A quantitative metric was developed to compare conservation of the human and mouse interactomes. In particular, a modification of the MARINa algorithm was developed that allows for single-sample analysis to infer the differential activity of 2028 transcriptional regulators represented in both interactomes on a sample-by-sample basis, from the expression of their interactome-specific targets. The analysis was performed on 1009 expression profiles representing 4 human datasets listed in the Table of FIG. 5, as well as across the mouse datasets, to determine whether the activity of each regulator, inferred either from the expression of its human interactome targets or its murine interactome targets, was significantly correlated (p≦0.05), indicating that the murine and human regulatory programs were therefore conserved. The accuracy of this metric was demonstrated by comparing two equivalent same-species interactomes from the human and mouse datasets (i.e., positive control), in which virtually all transcriptional regulators were conserved (>90%), contrasting with randomized interactomes (i.e., negative control) that had virtually no conservation. Histogram (density plots) showed the distribution of the correlation coefficients of activity profiles of transcriptional regulators for randomized interactomes (negative control) and the positive control interactomes for human and mouse. The degree of correlations was measured by the Z-score, and the Spearman correlation coefficient. The Z-score, also called the standard score, is the (signed) number of standard deviations an observation or datum is above the mean; and, is useful in comparing different populations. The Spearman's rank correlation coefficient, also called Spearman's rho, is a nonparametric measure of statistical dependence between two variables. It assesses how well the relationship between two variables can be described using a monotonic function. If there are no repeated data values, a perfect Spearman correlation of +1 or −1 occurs when each of the variables is a perfect monotone function of the other.

Using these metrics, it was found that 70% of the transcriptional regulators in the human and mouse prostate cancer interactomes regulate statistically conserved programs (p≦0.05). FIG. 2B is a graph that illustrates example percentage of the interactomes that are conserved between human and mouse models with prostate cancer, according to an embodiment. This histogram shows the distribution of the Z-scores for conservation of activity profiles between the human and mouse interactomes at p≦0.05. Comparison of the androgen receptor (AR) activity levels in each sample from Taylor et al. and the mouse dataset was performed using the Spearman correlation coefficient.

Notably, conserved transcriptional regulators included many genes known to play important roles in prostate cancer, such as AR, ETS 1, ETV4, ETV5, STAT3, MYC, BRCA1, and NKX3.1. In particular, AR displayed extensive correlation of its transcriptional activity between the human and mouse interactomes, consistent with its known role as a key regulator of prostate development and prostate tumorigenesis.

Master Regulators

The Master Regulator Inference algorithm (MARINa) (Carro et al., 2010; Lefebvre et al., 2010) was then used to infer candidate master regulators (MRs) that act individually or synergistically to drive malignant prostate cancer in the conserved interactomes. MARINa estimates differential activity (DA) based on enrichment (differential expression, DE) of their activated and repressed targets in the malignancy signature. More specifically, MARINa identified candidate MRs based on the concerted differential expression of their ARACNe-inferred targets (i.e., their differential activity, DA). Specifically, “activated” MRs have positively-regulated and repressed targets significantly enriched among upregulated and downregulated genes, respectively, while “repressed” MRs have the converse.

To interrogate the human prostate cancer interactome, a gene signature was used representing prostate cancer malignancy from the Taylor dataset, which compares aggressive prostate tumors (Gleason score>8 with rapid biochemical recurrence; sample size n=10) versus indolent ones (Gleason score 6 tumors with no biochemical recurrence; sample size n=39). These analyses identified 175 candidate MRs, including 49 activated and 126 repressed (p≦0.05).

To investigate the robustness of these MRs, MARINa was performed using a second, independent malignancy signature from the Balk dataset (see the table of FIG. 5), which compares lethal CRPC (sample size n=29) with indolent, hormone-naïve prostate cancer (sample size n=22). These independent MR analyses significantly overlapped with those identified from the Taylor malignancy signature (36 MRs in common; Fisher exact test p<0.0001). The Fisher exact test was used to compare two populations with the same number of members and determine the probability p that deviations from the null hypothesis, here that the two distributions are the same could be explained by random events. Furthermore, MARINa analyses of 15 independent interactomes using the Taylor human prostate cancer malignancy signature showed that the inferred MRs were highly overlapping with those inferred from two additional independent prostate cancer interactomes (p<7×10⁻⁹ and p<8×10⁻²⁰, Fisher exact test) but not with MRs inferred from non-prostate cancer specific interactomes (13 orders of magnitude different in significance). Thus, inference of master regulators of human prostate cancer malignancy required a prostate cancer-specific interactome but was independent of the specific dataset used for its interrogation.

To identify a corresponding mouse malignancy signature, MARINa was performed on four independent GEMM signatures, which are associated with prostate cancer malignancy and represent the diverse range of prostate cancer phenotypes represented among the GEMMs, including the NPK, NPB, NP, NP-AI, Myc, and NP53 mouse models. Meta-analyses of independent MR lists from these four independent GEMM signatures led to the identification of 229 candidate mouse MRs, including 110 activated and 119 repressed MRs (p≦0.001).

Conserved MRs were More Likely to be Associated with Disease Outcome than the Non-Conserved Ones

The resulting independent lists of human and mouse MRs were then integrated to produce a ranked list of 20 conserved MRs, including 7 activated and 13 repressed (joint p-value: p≦0.0074 by Stouffer's method). FIG. 3A is a Venn diagram and table that illustrates example selection of a subset of master regulators from a full set determined by available automated computer processes, according to an embodiment. Notably, these conserved MRs were more likely to be associated with disease outcome than the non-conserved ones, as assessed by a univariate COX proportional hazard regression model (43% versus 21%; p≦0.05), and were also more likely to be differentially expressed in aggressive prostate tumors (metastatic versus non-metastatic; 100% versus 60%).

Subsequent analysis focused on the subset of activated conserved MRs, each of which has been associated with cancer-related biological processes: CHAF1A (chromatin activity); TRIB3 (regulation of cell signaling in transcriptional control); FOXM1 (cell cycle progression); CENPF (mitosis); PSRC1 (growth control); TSFM (translational elongation); and ASF1B (regulation of nucleosome assembly). FIG. 3B is a diagram that illustrates example ranking of activated master regulators for their impacts on prostate cancer, according to an embodiment. Conserved activated MRs are shown for the human (left) and mouse (right) malignancy signatures, depicting the different positive (activated; upper bars) and negative (repressed; lower bars) targets. The ranks of differential activity (DA) and differential expression (DE) are shown by the shaded boxes; the numbers indicate the rank of the DE in the signature. Differential expression is defined by comparing expression levels of a gene between two groups of samples (here, aggressive and indolent prostate cancer samples) using the t-test. Genes ranked (i.e., sorted from the most over-expressed to the most under-expressed) by their differential expression define a signature. For example, 411 represents a higher position in the signature and thus a stronger differential expression, compared to 13323.

FIG. 3C is a table that illustrates example ranking of master regulators for their impact on prostate cancer by various available algorithms, according to an embodiment. In this summary of conserved MRs are shown: joint p-value from human and mouse MARINa analysis, calculated using Stouffer's method; p-value for COX proportional hazard regression model applied to mRNA expression levels and predicted MR activity; and average p-values for differential expression of MRs in metastatic versus non-metastatic primary tumors. Smaller p values means that the deviations from the null hypothesis, that the regulator is not important, are less likely due to chance and thus the corresponding regulator is more significant contributors. FOXM1 and CENPF are significant (p<0.05) for all measures.

Synergistic Master Regulators FOXM1 and CENPF are Differentially Expressed in Aggressive Prostate Tumors

These MRs were further prioritized by computationally evaluating their potential synergistic interactions. By these criteria, any pair of MRs was considered “synergistic” if their co-regulated ARACNe-inferred targets were significantly more enriched in the malignancy signature than their individual targets (p≦0.001) (Carro et al., 2010; Lefebvre et al., 2010). Using this computational approach to analyze all 21 possible pairs among the conserved activated MRs, the only pair that was found to be statistically significant was FOXM1 and CENPF.

FIG. 3D is a table that illustrates example predicted synergy of FOXM1 And CENPF among other pairs in the subset of master regulators using available algorithms, according to an embodiment. Shown are synergy p-values (i.e., enrichment of shared versus non-shared targets in the malignancy signature) for conserved MRs, inferred by MARINa. Clearly, the synergy of FOXM1 and CENPF is least likely to be random (p<0.001), and thus most significant.

5.3 Example 3 Method to Discover Synergistic Master Regulators of Phenotype Transitions

As demonstrated above, genome-wide cross-species interrogation of regulatory networks represents a valuable new strategy to identify causal mechanisms of human cancer. It is here proposed that analysis of genome-wide, cross-species regulatory networks provides an effective new paradigm for elucidating causal mechanisms of other complex diseases and phenotype transitions in general. FIG. 4 is a flow chart that illustrates an example method for determining various synergistic master regulators for other phenotype transitions, according to an embodiment. Although steps are depicted in FIG. 4 as integral steps in a particular order for purposes of illustration, in other embodiments, one or more steps, or portions thereof, are performed in a different order, or overlapping in time, in series or in parallel, or are omitted, or one or more additional steps are added, or the method is changed in some combination of ways.

In step 401, a gene expression profile dataset of one or more gene expression profiles is determined for human tissue in a context of interest (e.g., a prostate cancer). In step 403, based on said expression profile dataset, an interactome of human tissue in the context of interest is determined automatically on a processor (e.g., using ARACNe, or Context Likelihood of Relatedness (CLR), or Bayesian-networks algorithms as described in Akavia et al., 2010; Faith et al., 2007). In step 405, a gene expression profile dataset of one or more gene expression profiles is determined for animal tissue in a context of interest (e.g., murine prostate cancer) from multiple in vivo perturbations of one or more genetically distinct animals (e.g., mouse transgenic models of prostate cancer). Hereinafter for convenience, these gene expression profiles are termed an animal model gene expression dataset. The perturbations are performed to extend the dynamic range of cellular interactions beyond what is known or can be tried in human subjects. In step 407, based on animal tissue in the same context expression profiles, an interactome of animal cell context is determined automatically on a processor (e.g., using ARACNe, CLR, and Bayesian Networks).

In step 409, a cellular signature is generated. The cellular signature represents a cell phenotype transition of interest from a first phenotype to a second phenotype (e.g., normal cell→cancer cell or, as in the embodiment illustrated above, indolent prostate cancer→aggressive prostate cancer). At least one gene expression profile in the dataset is associated with the first phenotype, and at least one other gene expression profile in the dataset is associated with the second phenotype. The signature is a ranked list of genes sorted from the most under- to the most over-expressed in the second cellular phenotype (e.g. aggressive prostate cancer) compared to the first cellular phenotypes (e.g. indolent prostate cancer), as computed by a differential expression analysis algorithm (e.g., t-test, u-test, etc.), as well as the statistical significance of their differential expression (i.e., p-value, z-score, or others).

In step 413, one or more master regulator molecules (genes or corresponding proteins) are determined automatically on a processor (e.g., using MARINa). The MARINa algorithm uses the interactome to address the following question: which are the proteins in the interactome that are most likely to have produced the cellular signature and hence the phenotype transition. This analysis is performed independently for a signature representing an animal model cell state transition and an animal model interactome and for a signature representing a human cell state transition and a human interactome. That is, the interactome and the signature are from the same species. This is accomplished as follows for the human datasets. An analogous process is followed for the animal mode gene expression datasets and signatures.

Each protein in the human interactome is associated with its targets, i.e., the protein “regulon.” For each protein regulon the enrichment of the regulon genes is determined in genes that are differentially expressed in the human signature. The master regulators are based on the enrichment scores.

Enrichment is determined in various embodiments, using one or more of the following approaches, labeled A, B and C. Approach A is to determine whether the overlap between the statistically significant differentially expressed genes in the human signature (i.e., those with significant p-values, e.g. p≦0/05) and the protein regulon gene is statistically significant, using the Fisher's exact test, at a predefined significance threshold (e.g., p≦0.05). The master regulators are determined as those proteins with a statistically significant Fisher's exact test.

Approach B is to determine whether the normalized enrichment score (NES) representing the enrichment of the protein targets in differentially expressed human signature genes is statistically significant. The NES is the sum of (i) the normalized enrichment score (NES+) of the positive targets of the protein (e.g., those with Spearman correlation with the protein's associated gene expression above a predefined threshold, such as SC≧0) enrichment in over- or under-expressed human signature genes, determined by Gene Set Enrichment analysis algorithm or other equivalent algorithms and (ii) the normalized enrichment score (NES−) of the negative targets of the protein (e.g., those with Spearman correlation with the protein's associated gene expression below a predefined threshold, such as SC<0) enrichment in under- or over-expressed human signature genes, using the Gene Set Enrichment analysis algorithm or other equivalent algorithms. The positive master regulator (MR) proteins are determined as those proteins with a positive and statistically significant NES; and negative MR proteins are determined as those proteins with a negative and statistically significant NES.

Approach C is to determine whether a modified normalized enrichment score (NES) representing the enrichment of the protein targets in differentially expressed human signature genes is statistically significant. In approach C, the modified NES is the sum of (i) the NES+ of positive targets as determined by probabilistic analysis of their Spearman correlation (ii) the NES− of negative targets as determined by probabilistic analysis of their Spearman correlation and (iii) the NES= of targets that cannot be assigned to either the positive or negative target set of the protein in differentially expressed genes, regardless of their over or under expression. The positive master regulator (MR) proteins are determined as those proteins with a positive and statistically significant modified NES; and negative MR proteins are determined as those proteins with a negative and statistically significant modified NES.

Step 415 includes determining, manually or automatically on a processor, MRs common to interactomes of both human and animal models. For example, a novel modification of the MARINa algorithm is used, which allows for single-sample analysis to infer the differential activity of all transcriptional regulators represented in both interactomes (e.g., 2028 transcriptional regulators in the prostate interactomes) on a sample-by-sample basis, from the expression of their interactome-specific targets. In this novel process a protein P is selected. Then, the human regulon of P is identified from the human interactome and designated R_(H); and, the animal model regulon of P from the animal model interactome and designated R_(M). From a set of samples (1 . . . N) in a large dataset of both human and animal model gene expression profiles, a vector is determined that represents the corresponding human interactome specific differential activity of P, designated A_(H), using the R_(H) regulon genes, and a second vector is determined that represents the corresponding animal model specific differential activity of P, designated A_(M) using the R_(M) regulon genes. The vector A_(H) is determined by computing the normalized enrichment score (NES or modified NES, described above) of the R_(H) genes in genes that are differentially expressed in the human signature on each gene expression profile in the dataset. The vector A_(M) is determined by computing the normalized enrichment score (NES or modified NES, described above) of the R_(H) genes in genes that are differentially expressed in the animal model signature on each gene expression profile in the dataset. The Fisher exact test was used to compare the observed and expected MR overlap and determined the probability p that deviations from the null hypothesis, here that the observed and the expected overlap are the same, could be explained by random events.

Then, it is determined, automatically on a processor, whether the activity vectors of each regulator, inferred either from its human interactome targets A_(H) or from its animal model targets AM, are significantly correlated (e.g., p≦0.05 by Pearson or Spearman correlation). If so, the protein program is conserved across species, and the animal model experiments involving the study of P in the animal model are applicable to human subjects.

In step 417 it is determined, automatically on a processor, those that are synergistic, e.g., using MARINa. This step assesses whether the NES of the targets regulated by both proteins (i.e., the intersection of their regulons) is statistically significantly greater than the NES of either protein regulon.

In step 431, experiments are conducted to determine pattern of coexpression of synergistic master regulator molecules in tissue samples of transitioned phenotype (e.g., aggressive prostate cancer) compared to a pattern of coexpression of synergistic molecules in tissue samples of non-transitioning phenotype (e.g., persistently benign prostate tumors, called “indolent tumors” herein). In step 433, it is determined, manually or automatically using a processor, whether there are significantly different levels of coexpression in the two groups (transitioning and non-transitioning). If not, the process ends; or, control returns to step 409 to try a different set of synergistic master regulators common to all interactomes. Otherwise control passes to step 435.

In step 435, thresholds are determined and pattern of coexpression of master regulators or targets are used as indicators of human cell phenotype transition (e.g., aggressive prostate cancer). It is also determined whether suppression of two or more synergistic MRs leads to major abrogation of phenotype transition. If so, then, in step 437, a subject is treated by inhibiting expression of two or more synergistic master regulator molecules. Then the process ends, or is repeated.

Following the independent analyses of human and mouse master regulators, conserved master regulators were defined as those that were statistically significant (p≦0.05) in both the human and mouse analysis and thus had an integrated p-value (by Stouffer's method) p≦0.0074.

This general approach for evaluating conservation of regulatory networks can be used for comparative, cross-species analyses of regulatory networks for other cancers or other diseases and can be easily adapted to cross-species analyses of networks reverse-engineered with alternative algorithms, such as those based on the Context Likelihood of Relatedness (CLR) and Bayesian-networks algorithms (Akavia et al., 2010; Faith et al., 2007). Indeed, it is envisioned that the ability to quantitatively evaluate conservation of cross-species regulatory programs will be broadly applicable for other physiological and pathological comparisons, and particularly beneficial for accurate integration of pre-clinical findings from genetically engineered mice to human clinical trials.

Computational Hardware Overview

FIG. 12 is a block diagram that illustrates a computer system 1200 upon which an embodiment of the invention may be implemented. Computer system 1200 includes a communication mechanism such as a bus 1210 for passing information between other internal and external components of the computer system 1200. Information is represented as physical signals of a measurable phenomenon, typically electric voltages, but including, in other embodiments, such phenomena as magnetic, electromagnetic, pressure, chemical, molecular, atomic and quantum interactions. For example, north and south magnetic fields, or a zero and non-zero electric voltage, represent two states (0, 1) of a binary digit (bit). Other phenomena can represent digits of a higher base. A superposition of multiple simultaneous quantum states before measurement represents a quantum bit (qubit). A sequence of one or more digits constitutes digital data that is used to represent a number or code for a character. In some embodiments, information called analog data is represented by a near continuum of measurable values within a particular range. Computer system 1200, or a portion thereof, constitutes a means for performing one or more steps of one or more methods described herein.

A sequence of binary digits constitutes digital data that is used to represent a number or code for a character. A bus 1210 includes many parallel conductors of information so that information is transferred quickly among devices coupled to the bus 1210. One or more processors 1202 for processing information are coupled with the bus 1210. A processor 1202 performs a set of operations on information. The set of operations include bringing information in from the bus 1210 and placing information on the bus 1210. The set of operations also typically include comparing two or more units of information, shifting positions of units of information, and combining two or more units of information, such as by addition or multiplication. A sequence of operations to be executed by the processor 1202 constitutes computer instructions.

Computer system 1200 also includes a memory 1204 coupled to bus 1210. The memory 1204, such as a random access memory (RAM) or other dynamic storage device, stores information including computer instructions. Dynamic memory allows information stored therein to be changed by the computer system 1200. RAM allows a unit of information stored at a location called a memory address to be stored and retrieved independently of information at neighboring addresses. The memory 1204 is also used by the processor 1202 to store temporary values during execution of computer instructions. The computer system 1200 also includes a read only memory (ROM) 1206 or other static storage device coupled to the bus 1210 for storing static information, including instructions, that is not changed by the computer system 1200. Also coupled to bus 1210 is a non-volatile (persistent) storage device 1208, such as a magnetic disk or optical disk, for storing information, including instructions, that persists even when the computer system 1200 is turned off or otherwise loses power.

Information, including instructions, is provided to the bus 1210 for use by the processor from an external input device 1212, such as a keyboard containing alphanumeric keys operated by a human user, or a sensor. A sensor detects conditions in its vicinity and transforms those detections into signals compatible with the signals used to represent information in computer system 1200. Other external devices coupled to bus 1210, used primarily for interacting with humans, include a display device 1214, such as a cathode ray tube (CRT) or a liquid crystal display (LCD), for presenting images, and a pointing device 1216, such as a mouse or a trackball or cursor direction keys, for controlling a position of a small cursor image presented on the display 1214 and issuing commands associated with graphical elements presented on the display 1214.

In the illustrated embodiment, special purpose hardware, such as an application specific integrated circuit (IC) 1220, is coupled to bus 1210. The special purpose hardware is configured to perform operations not performed by processor 1202 quickly enough for special purposes. Examples of application specific ICs include graphics accelerator cards for generating images for display 1214, cryptographic boards for encrypting and decrypting messages sent over a network, speech recognition, and interfaces to special external devices, such as robotic arms and medical scanning equipment that repeatedly perform some complex sequence of operations that are more efficiently implemented in hardware.

Computer system 1200 also includes one or more instances of a communications interface 1270 coupled to bus 1210. Communication interface 1270 provides a two-way communication coupling to a variety of external devices that operate with their own processors, such as printers, scanners and external disks. In general the coupling is with a network link 1278 that is connected to a local network 1280 to which a variety of external devices with their own processors are connected. For example, communication interface 1270 may be a parallel port or a serial port or a universal serial bus (USB) port on a personal computer. In some embodiments, communications interface 1270 is an integrated services digital network (ISDN) card or a digital subscriber line (DSL) card or a telephone modem that provides an information communication connection to a corresponding type of telephone line. In some embodiments, a communication interface 1270 is a cable modem that converts signals on bus 1210 into signals for a communication connection over a coaxial cable or into optical signals for a communication connection over a fiber optic cable. As another example, communications interface 1270 may be a local area network (LAN) card to provide a data communication connection to a compatible LAN, such as Ethernet. Wireless links may also be implemented. Carrier waves, such as acoustic waves and electromagnetic waves, including radio, optical and infrared waves travel through space without wires or cables. Signals include man-made variations in amplitude, frequency, phase, polarization or other physical properties of carrier waves. For wireless links, the communications interface 1270 sends and receives electrical, acoustic or electromagnetic signals, including infrared and optical signals, which carry information streams, such as digital data.

The term computer-readable medium is used herein to refer to any medium that participates in providing information to processor 1202, including instructions for execution. Such a medium may take many forms, including, but not limited to, non-volatile media, volatile media and transmission media. Non-volatile media include, for example, optical or magnetic disks, such as storage device 1208. Volatile media include, for example, dynamic memory 1204. Transmission media include, for example, coaxial cables, copper wire, fiber optic cables, and waves that travel through space without wires or cables, such as acoustic waves and electromagnetic waves, including radio, optical and infrared waves. The term computer-readable storage medium is used herein to refer to any medium that participates in providing information to processor 1202, except for transmission media.

Common forms of computer-readable media include, for example, a floppy disk, a flexible disk, a hard disk, a magnetic tape, or any other magnetic medium, a compact disk ROM (CD-ROM), a digital video disk (DVD) or any other optical medium, punch cards, paper tape, or any other physical medium with patterns of holes, a RAM, a programmable ROM (PROM), an erasable PROM (EPROM), a FLASH-EPROM, or any other memory chip or cartridge, a carrier wave, or any other medium from which a computer can read. The term non-transitory computer-readable storage medium is used herein to refer to any medium that participates in providing information to processor 1202, except for carrier waves and other signals.

Logic encoded in one or more tangible media includes one or both of processor instructions on a computer-readable storage media and special purpose hardware, such as ASIC 1220.

Network link 1278 typically provides information communication through one or more networks to other devices that use or process the information. For example, network link 1278 may provide a connection through local network 1280 to a host computer 1282 or to equipment 1284 operated by an Internet Service Provider (ISP). ISP equipment 1284 in turn provides data communication services through the public, world-wide packet-switching communication network of networks now commonly referred to as the Internet 1290. A computer called a server 1292 connected to the Internet provides a service in response to information received over the Internet. For example, server 1292 provides information representing video data for presentation at display 1214.

The invention is related to the use of computer system 1200 for implementing the techniques described herein. According to one embodiment of the invention, those techniques are performed by computer system 1200 in response to processor 1202 executing one or more sequences of one or more instructions contained in memory 1204. Such instructions, also called software and program code, may be read into memory 1204 from another computer-readable medium such as storage device 1208. Execution of the sequences of instructions contained in memory 1204 causes processor 1202 to perform the method steps described herein. In alternative embodiments, hardware, such as application specific integrated circuit 1220, may be used in place of or in combination with software to implement the invention. Thus, embodiments of the invention are not limited to any specific combination of hardware and software.

The signals transmitted over network link 1278 and other networks through communications interface 1270, carry information to and from computer system 1200.

Computer system 1200 can send and receive information, including program code, through the networks 1280, 1290 among others, through network link 1278 and communications interface 1270. In an example using the Internet 1290, a server 1292 transmits program code for a particular application, requested by a message sent from computer 1200, through Internet 1290, ISP equipment 1284, local network 1280 and communications interface 1270. The received code may be executed by processor 1202 as it is received, or may be stored in storage device 1208 or other non-volatile storage for later execution, or both. In this manner, computer system 1200 may obtain application program code in the form of a signal on a carrier wave.

Various forms of computer readable media may be involved in carrying one or more sequence of instructions or data or both to processor 1202 for execution. For example, instructions and data may initially be carried on a magnetic disk of a remote computer such as host 1282. The remote computer loads the instructions and data into its dynamic memory and sends the instructions and data over a telephone line using a modem. A modem local to the computer system 1200 receives the instructions and data on a telephone line and uses an infra-red transmitter to convert the instructions and data to a signal on an infra-red a carrier wave serving as the network link 1278. An infrared detector serving as communications interface 1270 receives the instructions and data carried in the infrared signal and places information representing the instructions and data onto bus 1210. Bus 1210 carries the information to memory 1204 from which processor 1202 retrieves and executes the instructions using some of the data sent with the instructions. The instructions and data received in memory 1204 may optionally be stored on storage device 1208, either before or after execution by the processor 1202.

6. Alternatives and Extensions

In the foregoing specification, the invention has been described with reference to specific embodiments thereof. It will, however, be evident that various modifications and changes may be made thereto without departing from the broader spirit and scope of the invention. The specification and drawings are, accordingly, to be regarded in an illustrative rather than a restrictive sense. Throughout this specification and the claims, unless the context requires otherwise, the word “comprise” and its variations, such as “comprises” and “comprising,” will be understood to imply the inclusion of a stated item, element or step or group of items, elements or steps but not the exclusion of any other item, element or step or group of items, elements or steps. Furthermore, the indefinite article “a” or “an” is meant to indicate one or more of the item, element or step modified by the article.

7. References

Reference to the following publications can be found herein.

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What is claimed is:
 1. A method for treating prostate cancer or preventing the progression of a nonaggressive form of prostate cancer to an aggressive form, in a mammal, comprising administering to the mammal a therapeutically effective amount of one or more active agents that reduce the expression or biological activity of both Forkhead box protein M1 (FOXM1) (SEQ ID NO: 50) and Centromere protein F (CENPF) (SEQ ID NO: 54) or biologically active fragments thereof or biologically active fragments thereof selected from the group consisting of an isolated shRNA, siRNA, antisense RNA, antisense DNA, Chimeric Antisense DNA/RNA, microRNA, and ribozymes that are sufficiently complementary to either a gene or an mRNA encoding either FOXM1 or CENPF proteins.
 2. The method of claim 1, wherein the prostate cancer is aggressive prostate cancer.
 3. The method of claim 1, wherein the active agent is administered orally.
 4. The method of claim 1, wherein the active agent is administered locally to a prostate gland or prostate tumor.
 5. The method of claim 1, wherein the active agent is selected from the group consisting of FOXM1 shRNA#1 SEQ ID NO: 1, FOXM1 shRNA#2 SEQ ID NO: 2; CENPFshRNA#1 SEQ ID NO: 3; CENPFshRNA#2 SEQ ID NO:
 4. 6. A pharmaceutical formulation for treating prostate cancer or reducing or preventing the progression of a nonaggressive form of prostate cancer to an aggressive form, comprising a therapeutically effective amount of one or more active agents that reduce the expression or biological activity of both Forkhead box protein M1 (FOXM1) (SEQ ID NO: 50) and Centromere protein F: (CENPF) (SEQ ID NO: 54) selected from the group consisting of an isolated shRNA, siRNA, antisense RNA, antisense DNA, Chimeric Antisense DNA/RNA, microRNA, and ribozymes that are sufficiently complementary to either a gene or an mRNA encoding the FOXM1 or CENPF protein.
 7. The pharmaceutical composition of claim 5, wherein the therapeutically effective amount is an amount that produces an effect selected from the group consisting of reducing prostate tumor size, reducing prostate tumor growth, reducing or preventing the progression of a nonaggressive form of prostate cancer to an aggressive form, and metastasizing to a tumor in a different tissue.
 8. The pharmaceutical formulation of claim 6, wherein the active agent is selected from the group consisting of FOXM1 shRNA#1 SEQ ID NO: 1, FOXM1 shRNA#2 SEQ ID NO: 2; CENPFshRNA#1 SEQ ID NO: 3; CENPFshRNA#2 SEQ ID NO:
 4. 9. A medicament treating prostate cancer or reducing or preventing the progression of a nonaggressive form of prostate cancer to an aggressive form, comprising one or more active agents in a therapeutically effective amount that reduce the expression or biological activity of both Forkhead box protein M1 (FOXM1) (SEQ ID NO: 50) and Centromere protein F (CENPF) (SEQ ID NO: 54) or biologically active fragments thereof selected from the group consisting of an isolated shRNA, siRNA, antisense RNA, antisense DNA, Chimeric Antisense DNA/RNA, microRNA, and ribozymes that are sufficiently complementary to either a gene or an mRNA encoding either FOXM1 or CENPF proteins.
 10. The medicament of claim 9, wherein the active agent is selected from the group consisting of FOXM1 shRNA#1 SEQ ID NO: 1, FOXM1 shRNA#2 SEQ ID NO: 2; CENPFshRNA#1 SEQ ID NO: 3; CENPFshRNA#2 SEQ ID NO:
 4. 11. A method comprising: (a) receiving, automatically on a processor, data that indicates human gene expression profiles for human tissue in a context of interest comprising a plurality of cell phenotypes including at least one gene expression profile representing a first cell phenotype and at least one other gene expression profile representing a second cell phenotype; (b) determining, automatically on a processor based on the human gene expression profiles, data that indicates an interactome of human tissue in the context of interest; (c) determining, automatically on a processor based on the human gene expression profile, data that indicates a human signature that represents a ranking of genes differentially expressed in the second cell phenotype compared to the first cell phenotype; (d) determining, automatically on a processor based on the interactome of human tissue and the human signature, data that indicates human master regulator molecules most likely to have produced the human signature; (e) receiving, automatically on a processor, data that indicates animal model gene expression profiles for animal tissue in the context of interest based on multiple in vivo perturbations of one or more genetically distinct animals including at least one gene expression profile representing the first cell phenotype and at least one other gene expression profile representing the second cell phenotype; (f) determining, automatically on a processor based on the animal model gene expression profile, data that indicates an interactome of animal tissue in the context of interest; (g) determining, automatically on a processor based on the animal model gene expression profile, data that indicates an animal signature that represents a ranking of genes differentially expressed in the second cell phenotype compared to the first cell phenotype; (h) determining, automatically on a processor based on the interactome of animal tissue and the animal signature, data that indicates animal master regulator molecules most likely to have produced the animal signature; and (i) determining, automatically on a processor based on the human master regulator molecule and the animal master regulator molecules, data that indicates conserved master regulator molecules that are most likely to have produced both the human signature and the animal signature. 